Added one test to see that input is accepted.
Fixes #3375
Change-Id: I0f64b386477b9a72f18c95fd977ac8cf5dbeeccd
:issue:`3377`
+Avoid overzealous program abort with orientation restraints
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+It could happen that mdrun would abort on checking orientation restraints in multiple
+molecules even though no restraints where applied to them.
+
+:issue:`3375`
+
Fixes for ``gmx`` tools
^^^^^^^^^^^^^^^^^^^^^^^
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int nmol;
while (const InteractionLists* il = gmx_mtop_ilistloop_next(iloop, &nmol))
{
- if (nmol > 1)
+ if (nmol > 1 && (*il)[F_ORIRES].size() > 0)
{
gmx_fatal(FARGS,
"Found %d copies of a molecule with orientation restrains while the current "
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
initialconstraints.cpp
interactiveMD.cpp
outputfiles.cpp
+ orires.cpp
pmetest.cpp
simulator.cpp
swapcoords.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Test for MD with orientation restraints
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+
+class OriresTestFixture : public MdrunTestFixture
+{
+protected:
+ OriresTestFixture();
+ ~OriresTestFixture() override;
+};
+
+OriresTestFixture::OriresTestFixture() {}
+
+OriresTestFixture::~OriresTestFixture() {}
+
+//! Test fixture for mdrun with orires
+typedef gmx::test::OriresTestFixture OriresTest;
+
+/* Check whether the orires function works. */
+TEST_F(OriresTest, OriresCanRun)
+{
+ runner_.useTopGroAndNdxFromDatabase("orires_1lvz");
+ const std::string mdpContents = R"(
+ dt = 0.002
+ nsteps = 10
+ tcoupl = Berendsen
+ tc-grps = System
+ tau-t = 0.5
+ ref-t = 300
+ constraints = h-bonds
+ cutoff-scheme = Verlet
+ orire = Yes
+ orire-fitgrp = backbone
+ )";
+ runner_.useStringAsMdpFile(mdpContents);
+
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ ::gmx::test::CommandLine oriresCaller;
+
+ // Do an mdrun with ORIRES enabled
+ ASSERT_EQ(0, runner_.callMdrun(oriresCaller));
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1\r
+ 215\r
+ 1ILE N 1 2.423 2.571 1.751 0.0936 -0.3219 -0.0355\r
+ 1ILE H1 2 2.471 2.606 1.669 -2.9915 0.2125 -1.7758\r
+ 1ILE H2 3 2.346 2.637 1.754 0.0150 -0.2794 -1.7958\r
+ 1ILE H3 4 2.488 2.574 1.828 -1.8243 0.9739 1.6753\r
+ 1ILE CA 5 2.390 2.431 1.722 -0.0040 -0.3102 0.0167\r
+ 1ILE HA 6 2.323 2.434 1.636 -0.2465 -1.2965 0.1610\r
+ 1ILE CB 7 2.514 2.348 1.691 0.1548 -0.0167 -0.1390\r
+ 1ILE HB 8 2.560 2.401 1.607 3.5618 -0.2132 1.4412\r
+ 1ILE CG2 9 2.614 2.337 1.805 0.0404 -1.1364 -0.1327\r
+ 1ILE HG21 10 2.712 2.313 1.764 -1.2409 -2.3870 -2.6543\r
+ 1ILE HG22 11 2.622 2.425 1.870 -1.9742 0.2679 -1.6710\r
+ 1ILE HG23 12 2.585 2.259 1.876 1.0656 -1.6613 -0.2640\r
+ 1ILE CG1 13 2.466 2.213 1.638 -0.1684 -0.4516 1.2294\r
+ 1ILE HG11 14 2.393 2.229 1.559 2.4089 2.0711 -0.8483\r
+ 1ILE HG12 15 2.429 2.151 1.720 -1.2108 -0.2315 0.9452\r
+ 1ILE CD 16 2.588 2.138 1.585 -0.4056 -0.1240 0.1927\r
+ 1ILE HD1 17 2.656 2.208 1.536 2.6377 -2.2144 1.1352\r
+ 1ILE HD2 18 2.636 2.088 1.669 0.0941 -0.2702 -0.1801\r
+ 1ILE HD3 19 2.542 2.076 1.508 -0.8460 1.5249 -0.9365\r
+ 1ILE C 20 2.302 2.367 1.828 -0.1261 -0.0840 0.0509\r
+ 1ILE O 21 2.217 2.288 1.788 -0.1254 -0.2860 0.4413\r
+ 2ARG N 22 2.313 2.403 1.957 0.3813 -0.2249 0.0459\r
+ 2ARG H 23 2.368 2.486 1.972 0.5336 0.3645 -3.1220\r
+ 2ARG CA 24 2.237 2.338 2.061 0.1502 0.1391 0.1040\r
+ 2ARG HA 25 2.259 2.231 2.065 -2.6348 -0.5011 1.6122\r
+ 2ARG CB 26 2.286 2.415 2.183 -0.6640 0.4800 0.2203\r
+ 2ARG HB1 27 2.248 2.516 2.168 -1.9093 -0.1917 -1.4780\r
+ 2ARG HB2 28 2.395 2.415 2.185 -0.6732 0.8448 1.2487\r
+ 2ARG CG 29 2.247 2.355 2.318 0.1107 -0.1795 0.1531\r
+ 2ARG HG1 30 2.276 2.250 2.327 -0.1239 -0.0974 2.6200\r
+ 2ARG HG2 31 2.139 2.355 2.332 -0.3872 -1.6470 -2.7549\r
+ 2ARG CD 32 2.306 2.435 2.433 0.4397 -0.4298 0.1617\r
+ 2ARG HD1 33 2.408 2.466 2.407 -0.0073 1.8954 0.9116\r
+ 2ARG HD2 34 2.304 2.379 2.526 1.7767 -2.1717 -0.7954\r
+ 2ARG NE 35 2.221 2.552 2.456 0.6417 -0.2564 0.0480\r
+ 2ARG HE 36 2.149 2.567 2.387 0.8932 1.5191 0.1445\r
+ 2ARG CZ 37 2.237 2.639 2.557 -0.2182 0.1165 -0.1247\r
+ 2ARG NH1 38 2.325 2.632 2.658 -0.2428 -0.1092 -0.1168\r
+ 2ARG HH11 39 2.403 2.568 2.659 0.0097 0.1379 2.7157\r
+ 2ARG HH12 40 2.307 2.692 2.737 -0.0540 1.5964 -1.3081\r
+ 2ARG NH2 41 2.150 2.740 2.566 0.7550 1.0205 -0.6821\r
+ 2ARG HH21 42 2.092 2.756 2.485 -0.5254 -0.5336 -0.1216\r
+ 2ARG HH22 43 2.168 2.809 2.638 3.1877 0.7170 -0.9288\r
+ 2ARG C 44 2.085 2.344 2.050 0.1568 -0.7156 -0.5178\r
+ 2ARG O 45 2.018 2.254 2.100 0.1123 -0.5463 -0.2711\r
+ 3GLU N 46 2.030 2.447 1.986 -0.0863 -0.6508 -0.2018\r
+ 3GLU H 47 2.107 2.506 1.957 2.5076 -2.7563 1.8233\r
+ 3GLU CA 48 1.892 2.459 1.943 -0.0791 0.2737 0.0090\r
+ 3GLU HA 49 1.837 2.448 2.037 -0.0446 -2.3690 -0.2034\r
+ 3GLU CB 50 1.865 2.601 1.894 -0.2581 0.1853 -0.1468\r
+ 3GLU HB1 51 1.917 2.622 1.801 -1.4334 0.8957 -0.6630\r
+ 3GLU HB2 52 1.907 2.668 1.969 0.3663 1.1113 -1.2777\r
+ 3GLU CG 53 1.716 2.632 1.880 -0.2972 0.0131 -0.1084\r
+ 3GLU HG1 54 1.660 2.592 1.965 -0.5576 0.8787 0.1337\r
+ 3GLU HG2 55 1.681 2.577 1.793 1.2727 -2.5557 0.7537\r
+ 3GLU CD 56 1.682 2.778 1.861 0.2056 0.1281 -0.1580\r
+ 3GLU OE1 57 1.769 2.867 1.852 0.0423 0.3023 -0.0305\r
+ 3GLU OE2 58 1.562 2.800 1.831 0.1337 -0.3582 -0.2334\r
+ 3GLU C 59 1.852 2.355 1.840 0.0033 0.3192 -0.0686\r
+ 3GLU O 60 1.749 2.291 1.855 0.2870 -0.1890 -0.2784\r
+ 4ASN N 61 1.934 2.319 1.741 0.0582 -0.4105 0.2369\r
+ 4ASN H 62 2.011 2.383 1.724 -0.7026 0.2943 -0.6897\r
+ 4ASN CA 63 1.924 2.204 1.654 0.6640 -0.3126 0.0317\r
+ 4ASN HA 64 1.832 2.201 1.597 -0.0998 -0.7187 1.2592\r
+ 4ASN CB 65 2.035 2.216 1.550 0.7497 -0.1563 0.1416\r
+ 4ASN HB1 66 2.138 2.213 1.585 0.6873 -2.0392 0.2656\r
+ 4ASN HB2 67 2.020 2.315 1.507 0.5996 -0.2743 -0.0752\r
+ 4ASN CG 68 2.028 2.114 1.438 0.6663 0.3106 -0.2822\r
+ 4ASN OD1 69 2.086 2.007 1.454 0.4121 0.2228 0.0416\r
+ 4ASN ND2 70 1.940 2.128 1.338 0.0395 -0.1433 0.2007\r
+ 4ASN HD21 71 1.873 2.204 1.335 0.1268 -0.0060 1.2169\r
+ 4ASN HD22 72 1.942 2.064 1.260 0.8502 -0.3474 0.3858\r
+ 4ASN C 73 1.927 2.076 1.737 0.0386 -0.2349 0.1798\r
+ 4ASN O 74 1.840 1.991 1.717 -0.0458 -0.3335 0.9355\r
+ 5LEU N 75 2.021 2.063 1.831 -0.0687 0.6090 0.4036\r
+ 5LEU H 76 2.094 2.132 1.831 -0.4774 1.1622 -2.5375\r
+ 5LEU CA 77 2.032 1.944 1.913 -0.0413 0.5320 0.2883\r
+ 5LEU HA 78 2.027 1.857 1.848 -2.4141 1.5946 -1.0762\r
+ 5LEU CB 79 2.166 1.955 1.987 0.1109 -0.0905 0.1059\r
+ 5LEU HB1 80 2.170 1.872 2.058 2.6174 0.6698 0.9454\r
+ 5LEU HB2 81 2.162 2.047 2.045 0.8089 0.5599 -0.8616\r
+ 5LEU CG 82 2.288 1.952 1.895 0.0512 -0.2565 0.0305\r
+ 5LEU HG 83 2.285 2.039 1.829 -0.4586 0.4334 0.9230\r
+ 5LEU CD1 84 2.408 1.964 1.988 0.0055 0.1775 0.0372\r
+ 5LEU HD11 85 2.407 1.877 2.053 0.0883 0.1450 -0.0054\r
+ 5LEU HD12 86 2.501 1.962 1.932 -0.4579 -1.7524 -0.7446\r
+ 5LEU HD13 87 2.402 2.060 2.041 1.9484 -0.0759 0.8026\r
+ 5LEU CD2 88 2.309 1.825 1.814 0.4229 -0.0957 -0.1266\r
+ 5LEU HD21 89 2.222 1.814 1.748 -1.5139 2.0474 1.8761\r
+ 5LEU HD22 90 2.406 1.834 1.765 0.0073 -2.6964 -1.5970\r
+ 5LEU HD23 91 2.313 1.735 1.875 0.0387 -1.7936 -2.4350\r
+ 5LEU C 92 1.915 1.936 2.010 -0.2894 0.1139 -0.0464\r
+ 5LEU O 93 1.876 1.826 2.049 -0.1455 -0.1880 -0.7352\r
+ 6LYS N 94 1.842 2.045 2.034 -0.6901 0.0243 -0.8226\r
+ 6LYS H 95 1.882 2.132 2.004 0.8199 -0.9562 -1.7789\r
+ 6LYS CA 96 1.719 2.046 2.110 -0.2719 0.1430 -0.1383\r
+ 6LYS HA 97 1.741 1.993 2.203 0.9730 -0.6169 -0.8467\r
+ 6LYS CB 98 1.672 2.187 2.146 -0.2506 0.0636 0.2090\r
+ 6LYS HB1 99 1.625 2.232 2.059 0.9820 2.6593 0.7788\r
+ 6LYS HB2 100 1.755 2.252 2.173 0.1270 -0.8653 1.3155\r
+ 6LYS CG 101 1.583 2.188 2.270 -0.3322 -0.0661 0.1524\r
+ 6LYS HG1 102 1.651 2.161 2.351 2.0085 2.7494 -0.6671\r
+ 6LYS HG2 103 1.497 2.122 2.264 0.2178 -0.8095 0.2702\r
+ 6LYS CD 104 1.541 2.333 2.293 0.4968 0.1971 0.0589\r
+ 6LYS HD1 105 1.522 2.376 2.195 1.7394 0.6881 0.0130\r
+ 6LYS HD2 106 1.620 2.389 2.343 0.0016 0.7250 0.2662\r
+ 6LYS CE 107 1.416 2.344 2.380 0.7798 0.1243 0.4757\r
+ 6LYS HE1 108 1.340 2.270 2.355 -1.1187 1.9929 0.4302\r
+ 6LYS HE2 109 1.363 2.437 2.361 -1.3895 -1.1540 -0.0331\r
+ 6LYS NZ 110 1.441 2.318 2.523 0.6853 0.4103 0.5445\r
+ 6LYS HZ1 111 1.361 2.279 2.570 -0.0921 1.4011 0.0796\r
+ 6LYS HZ2 112 1.513 2.248 2.533 0.3965 0.2699 1.8626\r
+ 6LYS HZ3 113 1.474 2.400 2.572 0.9530 0.7453 -0.1836\r
+ 6LYS C 114 1.609 1.980 2.028 -0.0506 0.3156 -0.5774\r
+ 6LYS O 115 1.522 1.915 2.087 -0.0003 0.4952 -0.3006\r
+ 7ASP N 116 1.606 1.984 1.895 0.1681 -0.2273 -0.5995\r
+ 7ASP H 117 1.664 2.055 1.852 1.5543 -1.5568 -1.0282\r
+ 7ASP CA 118 1.509 1.911 1.816 -0.1619 0.2418 -0.6279\r
+ 7ASP HA 119 1.413 1.911 1.868 -0.3314 1.7001 -0.8973\r
+ 7ASP CB 120 1.487 1.969 1.677 0.4599 -0.5002 -1.0444\r
+ 7ASP HB1 121 1.422 1.905 1.618 2.1452 -2.1706 -1.1680\r
+ 7ASP HB2 122 1.582 1.983 1.626 1.0920 1.4900 0.5546\r
+ 7ASP CG 123 1.437 2.112 1.663 0.1593 -0.4950 0.0059\r
+ 7ASP OD1 124 1.373 2.166 1.756 -0.4294 0.3704 -0.8781\r
+ 7ASP OD2 125 1.451 2.169 1.553 0.1888 0.3519 0.4321\r
+ 7ASP C 126 1.545 1.765 1.792 0.3318 0.3579 -0.5897\r
+ 7ASP O 127 1.461 1.686 1.750 -0.0629 0.1795 0.5235\r
+ 8SER N 128 1.670 1.724 1.815 0.2385 0.1590 -0.4441\r
+ 8SER H 129 1.747 1.787 1.832 1.7195 -1.6506 -0.0484\r
+ 8SER CA 130 1.707 1.584 1.799 -0.1400 -0.0362 0.3462\r
+ 8SER HA 131 1.666 1.564 1.700 2.3315 -0.8831 -0.5812\r
+ 8SER CB 132 1.859 1.565 1.798 -0.0427 0.6957 0.2654\r
+ 8SER HB1 133 1.905 1.636 1.730 -0.3410 -0.1665 -0.8636\r
+ 8SER HB2 134 1.879 1.464 1.763 0.7777 0.1943 2.0685\r
+ 8SER OG 135 1.909 1.562 1.930 0.2456 0.6083 0.1532\r
+ 8SER HG 136 1.910 1.652 1.963 -0.0997 1.1774 -1.3071\r
+ 8SER C 137 1.634 1.498 1.900 -0.3761 -0.0841 0.1342\r
+ 8SER O 138 1.618 1.379 1.872 -0.1086 -0.0425 -0.1938\r
+ 9GLY N 139 1.603 1.546 2.021 -0.8083 -0.0860 0.0251\r
+ 9GLY H 140 1.649 1.632 2.046 1.0775 -1.0793 0.1291\r
+ 9GLY CA 141 1.559 1.466 2.134 -0.2229 -0.2196 0.1597\r
+ 9GLY HA1 142 1.472 1.410 2.100 0.9214 0.4124 -4.5132\r
+ 9GLY HA2 143 1.531 1.537 2.212 1.0939 0.5737 -0.0511\r
+ 9GLY C 144 1.665 1.373 2.190 0.1423 0.1523 0.0935\r
+ 9GLY O 145 1.634 1.303 2.287 -0.4717 0.4476 0.1139\r
+ 10LEU N 146 1.786 1.358 2.135 -0.0857 0.0788 -0.3970\r
+ 10LEU H 147 1.810 1.425 2.063 0.9925 -0.8606 -0.9407\r
+ 10LEU CA 148 1.897 1.277 2.180 -0.2014 0.1010 -0.0670\r
+ 10LEU HA 149 1.856 1.189 2.229 -0.3069 -1.5412 -2.9031\r
+ 10LEU CB 150 1.971 1.232 2.055 -0.2947 0.0573 -0.1062\r
+ 10LEU HB1 151 2.052 1.171 2.097 -0.0778 0.7093 0.4427\r
+ 10LEU HB2 152 2.010 1.320 2.004 -0.2353 0.7669 1.1344\r
+ 10LEU CG 153 1.884 1.156 1.956 -0.1920 0.5272 -0.5642\r
+ 10LEU HG 154 1.806 1.212 1.904 -0.3825 -0.6450 -1.5878\r
+ 10LEU CD1 155 1.978 1.101 1.849 -0.0609 0.4181 -0.3931\r
+ 10LEU HD11 156 1.924 1.056 1.766 0.0468 -1.4596 0.5037\r
+ 10LEU HD12 157 2.043 1.175 1.802 1.6876 -0.3308 0.7317\r
+ 10LEU HD13 158 2.042 1.023 1.891 1.0543 1.5004 -0.0242\r
+ 10LEU CD2 159 1.808 1.046 2.029 0.7995 0.0120 -0.2899\r
+ 10LEU HD21 160 1.860 0.977 2.096 -1.4402 -1.0796 0.4376\r
+ 10LEU HD22 161 1.719 1.077 2.085 -1.6181 -2.6169 -2.3914\r
+ 10LEU HD23 162 1.761 0.986 1.951 -0.2814 -0.8529 0.9735\r
+ 10LEU C 163 1.986 1.354 2.278 -0.1641 -0.1064 0.0627\r
+ 10LEU O 164 2.078 1.295 2.334 -0.1827 -0.0007 0.2057\r
+ 11PHE N 165 1.966 1.484 2.299 -0.1651 -0.0363 -0.3616\r
+ 11PHE H 166 1.881 1.529 2.267 -1.5975 -1.4086 1.3043\r
+ 11PHE CA 167 2.063 1.574 2.359 -0.4167 -0.1086 0.1618\r
+ 11PHE HA 168 2.146 1.515 2.399 -0.9779 -0.5706 0.6735\r
+ 11PHE CB 169 2.128 1.654 2.247 -0.7180 -0.2172 -0.0927\r
+ 11PHE HB1 170 2.145 1.758 2.274 -0.0255 -0.3036 -0.1819\r
+ 11PHE HB2 171 2.053 1.660 2.168 0.1930 0.2958 -0.9555\r
+ 11PHE CG 172 2.257 1.600 2.189 -0.3828 0.5005 -0.0355\r
+ 11PHE CD1 173 2.257 1.503 2.087 0.6644 0.5474 -0.0918\r
+ 11PHE HD1 174 2.159 1.478 2.048 -1.1761 4.0170 1.7102\r
+ 11PHE CE1 175 2.377 1.453 2.036 0.3452 -0.9590 0.5803\r
+ 11PHE HE1 176 2.376 1.385 1.951 0.5811 -0.1294 -0.1025\r
+ 11PHE CZ 177 2.497 1.479 2.103 0.4084 0.3115 0.0073\r
+ 11PHE HZ 178 2.589 1.435 2.067 -0.2225 -1.0535 -0.0223\r
+ 11PHE CE2 179 2.495 1.585 2.194 0.0892 -0.4109 0.8548\r
+ 11PHE HE2 180 2.591 1.614 2.233 -0.9734 0.2875 3.1320\r
+ 11PHE CD2 181 2.378 1.647 2.240 -0.1009 0.1958 -0.4170\r
+ 11PHE HD2 182 2.371 1.726 2.313 -0.8800 -0.3576 0.1153\r
+ 11PHE C 183 2.012 1.664 2.470 0.1919 0.0750 0.2944\r
+ 11PHE OC1 184 1.903 1.721 2.453 0.1210 -0.0696 0.2605\r
+ 11PHE OC2 185 2.078 1.675 2.576 -0.3707 0.4761 0.6025\r
+ 12SOL OW 186 3.873 0.044 3.044 -0.2983 0.3579 -0.0212\r
+ 12SOL HW1 187 3.929 0.094 2.984 2.4308 -0.0923 1.9919\r
+ 12SOL HW2 188 3.882 0.088 3.128 0.1698 -2.0064 1.2441\r
+ 13SOL OW 189 3.300 3.670 3.302 -0.2897 -0.5158 -0.1517\r
+ 13SOL HW1 190 3.229 3.716 3.346 -0.9753 -1.2956 -0.4340\r
+ 13SOL HW2 191 3.334 3.609 3.368 0.5166 0.2449 0.1700\r
+ 14SOL OW 192 3.835 3.670 1.359 0.5733 -0.4605 -0.0371\r
+ 14SOL HW1 193 3.783 3.614 1.302 1.2593 -2.0638 0.8277\r
+ 14SOL HW2 194 3.915 3.620 1.376 1.1344 0.7012 0.9362\r
+ 15SOL OW 195 0.782 2.741 1.583 0.3241 0.3358 0.3704\r
+ 15SOL HW1 196 0.759 2.784 1.666 -1.5933 -0.1989 0.1555\r
+ 15SOL HW2 197 0.713 2.677 1.569 -0.0345 1.1794 -2.2267\r
+ 16SOL OW 198 1.556 1.656 0.760 0.0766 0.1757 -0.0926\r
+ 16SOL HW1 199 1.602 1.738 0.744 1.4009 -0.7885 -1.6586\r
+ 16SOL HW2 200 1.626 1.592 0.772 -0.8985 -0.9048 -0.0060\r
+ 17SOL OW 201 3.141 3.132 3.392 0.0944 0.2707 0.1807\r
+ 17SOL HW1 202 3.169 3.112 3.481 1.0627 -0.8159 -0.3515\r
+ 17SOL HW2 203 3.073 3.068 3.373 -0.1843 0.5675 0.1572\r
+ 18SOL OW 204 0.105 1.434 0.498 -0.4822 -0.4474 -0.5695\r
+ 18SOL HW1 205 0.086 1.354 0.546 0.5427 0.0586 0.7387\r
+ 18SOL HW2 206 0.124 1.405 0.409 -0.4729 -1.6162 -0.2027\r
+ 19SOL OW 207 2.107 2.873 3.366 -0.2955 0.3323 -0.4196\r
+ 19SOL HW1 208 2.126 2.797 3.421 1.6975 0.3369 -1.0365\r
+ 19SOL HW2 209 2.096 2.945 3.429 -0.8651 -0.1900 0.0982\r
+ 20SOL OW 210 0.224 1.018 0.877 0.0313 0.0274 -0.5438\r
+ 20SOL HW1 211 0.137 0.989 0.853 -0.8808 2.0702 0.0306\r
+ 20SOL HW2 212 0.231 0.998 0.971 0.3370 -0.4605 -0.6666\r
+ 21SOL OW 213 2.917 1.502 3.799 0.1262 0.5285 0.2875\r
+ 21SOL HW1 214 2.887 1.585 3.762 -0.1020 0.2306 -0.2081\r
+ 21SOL HW2 215 2.963 1.458 3.728 -1.6917 -0.7588 -0.1707\r
+ 3.98279 3.98279 3.98279\r
--- /dev/null
+[ System ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
+ 211 212 213 214 215
+[ Backbone ]
+ 1 5 20 22 24 44 46 48 59 61 63 73 75 77 92
+ 94 96 114 116 118 126 128 130 137 139 141 144 146 148 163
+ 165 167 183
+[ SOL ]
+ 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200
+ 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
--- /dev/null
+;\r
+; File '1lvz.top' was generated\r
+; By user: anna (502)\r
+; On host: phy-freki.physics.uu.se\r
+; At date: Mon Feb 3 17:42:15 2020\r
+;\r
+; This is a standalone topology file\r
+;\r
+; Created by:\r
+; :-) GROMACS - gmx pdb2gmx, 2019.4 (-:\r
+; \r
+; Executable: /usr/local/gromacs/bin/gmx\r
+; Data prefix: /usr/local/gromacs\r
+; Working dir: /Users/anna/Git/NMRreader\r
+; Command line:\r
+; gmx -quiet pdb2gmx -f 1lvz.pdb -ignh -ff amber99sb-ildn -water tip3p -p 1lvz.top -o 1lvz.gro\r
+; Force field was read from the standard GROMACS share directory.\r
+;\r
+\r
+; Include forcefield parameters\r
+#include "amber99sb-ildn.ff/forcefield.itp"\r
+\r
+[ moleculetype ]\r
+; Name nrexcl\r
+Protein_chain_A 3\r
+\r
+[ atoms ]\r
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB\r
+; residue 1 ILE rtp NILE q +1.0\r
+ 1 N3 1 ILE N 1 0.0311 14.01\r
+ 2 H 1 ILE H1 2 0.2329 1.008\r
+ 3 H 1 ILE H2 3 0.2329 1.008\r
+ 4 H 1 ILE H3 4 0.2329 1.008\r
+ 5 CT 1 ILE CA 5 0.0257 12.01\r
+ 6 HP 1 ILE HA 6 0.1031 1.008\r
+ 7 CT 1 ILE CB 7 0.1885 12.01\r
+ 8 HC 1 ILE HB 8 0.0213 1.008\r
+ 9 CT 1 ILE CG2 9 -0.372 12.01\r
+ 10 HC 1 ILE HG21 10 0.0947 1.008\r
+ 11 HC 1 ILE HG22 11 0.0947 1.008\r
+ 12 HC 1 ILE HG23 12 0.0947 1.008\r
+ 13 CT 1 ILE CG1 13 -0.0387 12.01\r
+ 14 HC 1 ILE HG11 14 0.0201 1.008\r
+ 15 HC 1 ILE HG12 15 0.0201 1.008\r
+ 16 CT 1 ILE CD 16 -0.0908 12.01\r
+ 17 HC 1 ILE HD1 17 0.0226 1.008\r
+ 18 HC 1 ILE HD2 18 0.0226 1.008\r
+ 19 HC 1 ILE HD3 19 0.0226 1.008\r
+ 20 C 1 ILE C 20 0.6123 12.01\r
+ 21 O 1 ILE O 21 -0.5713 16 ; qtot 1\r
+; residue 2 ARG rtp ARG q +1.0\r
+ 22 N 2 ARG N 22 -0.3479 14.01\r
+ 23 H 2 ARG H 23 0.2747 1.008\r
+ 24 CT 2 ARG CA 24 -0.2637 12.01\r
+ 25 H1 2 ARG HA 25 0.156 1.008\r
+ 26 CT 2 ARG CB 26 -0.0007 12.01\r
+ 27 HC 2 ARG HB1 27 0.0327 1.008\r
+ 28 HC 2 ARG HB2 28 0.0327 1.008\r
+ 29 CT 2 ARG CG 29 0.039 12.01\r
+ 30 HC 2 ARG HG1 30 0.0285 1.008\r
+ 31 HC 2 ARG HG2 31 0.0285 1.008\r
+ 32 CT 2 ARG CD 32 0.0486 12.01\r
+ 33 H1 2 ARG HD1 33 0.0687 1.008\r
+ 34 H1 2 ARG HD2 34 0.0687 1.008\r
+ 35 N2 2 ARG NE 35 -0.5295 14.01\r
+ 36 H 2 ARG HE 36 0.3456 1.008\r
+ 37 CA 2 ARG CZ 37 0.8076 12.01\r
+ 38 N2 2 ARG NH1 38 -0.8627 14.01\r
+ 39 H 2 ARG HH11 39 0.4478 1.008\r
+ 40 H 2 ARG HH12 40 0.4478 1.008\r
+ 41 N2 2 ARG NH2 41 -0.8627 14.01\r
+ 42 H 2 ARG HH21 42 0.4478 1.008\r
+ 43 H 2 ARG HH22 43 0.4478 1.008\r
+ 44 C 2 ARG C 44 0.7341 12.01\r
+ 45 O 2 ARG O 45 -0.5894 16 ; qtot 2\r
+; residue 3 GLU rtp GLU q -1.0\r
+ 46 N 3 GLU N 46 -0.5163 14.01\r
+ 47 H 3 GLU H 47 0.2936 1.008\r
+ 48 CT 3 GLU CA 48 0.0397 12.01\r
+ 49 H1 3 GLU HA 49 0.1105 1.008\r
+ 50 CT 3 GLU CB 50 0.056 12.01\r
+ 51 HC 3 GLU HB1 51 -0.0173 1.008\r
+ 52 HC 3 GLU HB2 52 -0.0173 1.008\r
+ 53 CT 3 GLU CG 53 0.0136 12.01\r
+ 54 HC 3 GLU HG1 54 -0.0425 1.008\r
+ 55 HC 3 GLU HG2 55 -0.0425 1.008\r
+ 56 C 3 GLU CD 56 0.8054 12.01\r
+ 57 O2 3 GLU OE1 57 -0.8188 16\r
+ 58 O2 3 GLU OE2 58 -0.8188 16\r
+ 59 C 3 GLU C 59 0.5366 12.01\r
+ 60 O 3 GLU O 60 -0.5819 16 ; qtot 1\r
+; residue 4 ASN rtp ASN q 0.0\r
+ 61 N 4 ASN N 61 -0.4157 14.01\r
+ 62 H 4 ASN H 62 0.2719 1.008\r
+ 63 CT 4 ASN CA 63 0.0143 12.01\r
+ 64 H1 4 ASN HA 64 0.1048 1.008\r
+ 65 CT 4 ASN CB 65 -0.2041 12.01\r
+ 66 HC 4 ASN HB1 66 0.0797 1.008\r
+ 67 HC 4 ASN HB2 67 0.0797 1.008\r
+ 68 C 4 ASN CG 68 0.713 12.01\r
+ 69 O 4 ASN OD1 69 -0.5931 16\r
+ 70 N 4 ASN ND2 70 -0.9191 14.01\r
+ 71 H 4 ASN HD21 71 0.4196 1.008\r
+ 72 H 4 ASN HD22 72 0.4196 1.008\r
+ 73 C 4 ASN C 73 0.5973 12.01\r
+ 74 O 4 ASN O 74 -0.5679 16 ; qtot 1\r
+; residue 5 LEU rtp LEU q 0.0\r
+ 75 N 5 LEU N 75 -0.4157 14.01\r
+ 76 H 5 LEU H 76 0.2719 1.008\r
+ 77 CT 5 LEU CA 77 -0.0518 12.01\r
+ 78 H1 5 LEU HA 78 0.0922 1.008\r
+ 79 CT 5 LEU CB 79 -0.1102 12.01\r
+ 80 HC 5 LEU HB1 80 0.0457 1.008\r
+ 81 HC 5 LEU HB2 81 0.0457 1.008\r
+ 82 CT 5 LEU CG 82 0.3531 12.01\r
+ 83 HC 5 LEU HG 83 -0.0361 1.008\r
+ 84 CT 5 LEU CD1 84 -0.4121 12.01\r
+ 85 HC 5 LEU HD11 85 0.1 1.008\r
+ 86 HC 5 LEU HD12 86 0.1 1.008\r
+ 87 HC 5 LEU HD13 87 0.1 1.008\r
+ 88 CT 5 LEU CD2 88 -0.4121 12.01\r
+ 89 HC 5 LEU HD21 89 0.1 1.008\r
+ 90 HC 5 LEU HD22 90 0.1 1.008\r
+ 91 HC 5 LEU HD23 91 0.1 1.008\r
+ 92 C 5 LEU C 92 0.5973 12.01\r
+ 93 O 5 LEU O 93 -0.5679 16 ; qtot 1\r
+; residue 6 LYS rtp LYS q +1.0\r
+ 94 N 6 LYS N 94 -0.3479 14.01\r
+ 95 H 6 LYS H 95 0.2747 1.008\r
+ 96 CT 6 LYS CA 96 -0.24 12.01\r
+ 97 H1 6 LYS HA 97 0.1426 1.008\r
+ 98 CT 6 LYS CB 98 -0.0094 12.01\r
+ 99 HC 6 LYS HB1 99 0.0362 1.008\r
+ 100 HC 6 LYS HB2 100 0.0362 1.008\r
+ 101 CT 6 LYS CG 101 0.0187 12.01\r
+ 102 HC 6 LYS HG1 102 0.0103 1.008\r
+ 103 HC 6 LYS HG2 103 0.0103 1.008\r
+ 104 CT 6 LYS CD 104 -0.0479 12.01\r
+ 105 HC 6 LYS HD1 105 0.0621 1.008\r
+ 106 HC 6 LYS HD2 106 0.0621 1.008\r
+ 107 CT 6 LYS CE 107 -0.0143 12.01\r
+ 108 HP 6 LYS HE1 108 0.1135 1.008\r
+ 109 HP 6 LYS HE2 109 0.1135 1.008\r
+ 110 N3 6 LYS NZ 110 -0.3854 14.01\r
+ 111 H 6 LYS HZ1 111 0.34 1.008\r
+ 112 H 6 LYS HZ2 112 0.34 1.008\r
+ 113 H 6 LYS HZ3 113 0.34 1.008\r
+ 114 C 6 LYS C 114 0.7341 12.01\r
+ 115 O 6 LYS O 115 -0.5894 16 ; qtot 2\r
+; residue 7 ASP rtp ASP q -1.0\r
+ 116 N 7 ASP N 116 -0.5163 14.01\r
+ 117 H 7 ASP H 117 0.2936 1.008\r
+ 118 CT 7 ASP CA 118 0.0381 12.01\r
+ 119 H1 7 ASP HA 119 0.088 1.008\r
+ 120 CT 7 ASP CB 120 -0.0303 12.01\r
+ 121 HC 7 ASP HB1 121 -0.0122 1.008\r
+ 122 HC 7 ASP HB2 122 -0.0122 1.008\r
+ 123 C 7 ASP CG 123 0.7994 12.01\r
+ 124 O2 7 ASP OD1 124 -0.8014 16\r
+ 125 O2 7 ASP OD2 125 -0.8014 16\r
+ 126 C 7 ASP C 126 0.5366 12.01\r
+ 127 O 7 ASP O 127 -0.5819 16 ; qtot 1\r
+; residue 8 SER rtp SER q 0.0\r
+ 128 N 8 SER N 128 -0.4157 14.01\r
+ 129 H 8 SER H 129 0.2719 1.008\r
+ 130 CT 8 SER CA 130 -0.0249 12.01\r
+ 131 H1 8 SER HA 131 0.0843 1.008\r
+ 132 CT 8 SER CB 132 0.2117 12.01\r
+ 133 H1 8 SER HB1 133 0.0352 1.008\r
+ 134 H1 8 SER HB2 134 0.0352 1.008\r
+ 135 OH 8 SER OG 135 -0.6546 16\r
+ 136 HO 8 SER HG 136 0.4275 1.008\r
+ 137 C 8 SER C 137 0.5973 12.01\r
+ 138 O 8 SER O 138 -0.5679 16 ; qtot 1\r
+; residue 9 GLY rtp GLY q 0.0\r
+ 139 N 9 GLY N 139 -0.4157 14.01\r
+ 140 H 9 GLY H 140 0.2719 1.008\r
+ 141 CT 9 GLY CA 141 -0.0252 12.01\r
+ 142 H1 9 GLY HA1 142 0.0698 1.008\r
+ 143 H1 9 GLY HA2 143 0.0698 1.008\r
+ 144 C 9 GLY C 144 0.5973 12.01\r
+ 145 O 9 GLY O 145 -0.5679 16 ; qtot 1\r
+; residue 10 LEU rtp LEU q 0.0\r
+ 146 N 10 LEU N 146 -0.4157 14.01\r
+ 147 H 10 LEU H 147 0.2719 1.008\r
+ 148 CT 10 LEU CA 148 -0.0518 12.01\r
+ 149 H1 10 LEU HA 149 0.0922 1.008\r
+ 150 CT 10 LEU CB 150 -0.1102 12.01\r
+ 151 HC 10 LEU HB1 151 0.0457 1.008\r
+ 152 HC 10 LEU HB2 152 0.0457 1.008\r
+ 153 CT 10 LEU CG 153 0.3531 12.01\r
+ 154 HC 10 LEU HG 154 -0.0361 1.008\r
+ 155 CT 10 LEU CD1 155 -0.4121 12.01\r
+ 156 HC 10 LEU HD11 156 0.1 1.008\r
+ 157 HC 10 LEU HD12 157 0.1 1.008\r
+ 158 HC 10 LEU HD13 158 0.1 1.008\r
+ 159 CT 10 LEU CD2 159 -0.4121 12.01\r
+ 160 HC 10 LEU HD21 160 0.1 1.008\r
+ 161 HC 10 LEU HD22 161 0.1 1.008\r
+ 162 HC 10 LEU HD23 162 0.1 1.008\r
+ 163 C 10 LEU C 163 0.5973 12.01\r
+ 164 O 10 LEU O 164 -0.5679 16 ; qtot 1\r
+; residue 11 PHE rtp CPHE q -1.0\r
+ 165 N 11 PHE N 165 -0.3821 14.01\r
+ 166 H 11 PHE H 166 0.2681 1.008\r
+ 167 CT 11 PHE CA 167 -0.1825 12.01\r
+ 168 H1 11 PHE HA 168 0.1098 1.008\r
+ 169 CT 11 PHE CB 169 -0.0959 12.01\r
+ 170 HC 11 PHE HB1 170 0.0443 1.008\r
+ 171 HC 11 PHE HB2 171 0.0443 1.008\r
+ 172 CA 11 PHE CG 172 0.0552 12.01\r
+ 173 CA 11 PHE CD1 173 -0.13 12.01\r
+ 174 HA 11 PHE HD1 174 0.1408 1.008\r
+ 175 CA 11 PHE CE1 175 -0.1847 12.01\r
+ 176 HA 11 PHE HE1 176 0.1461 1.008\r
+ 177 CA 11 PHE CZ 177 -0.0944 12.01\r
+ 178 HA 11 PHE HZ 178 0.128 1.008\r
+ 179 CA 11 PHE CE2 179 -0.1847 12.01\r
+ 180 HA 11 PHE HE2 180 0.1461 1.008\r
+ 181 CA 11 PHE CD2 181 -0.13 12.01\r
+ 182 HA 11 PHE HD2 182 0.1408 1.008\r
+ 183 C 11 PHE C 183 0.766 12.01\r
+ 184 O2 11 PHE OC1 184 -0.8026 16\r
+ 185 O2 11 PHE OC2 185 -0.8026 16 ; qtot 0\r
+\r
+[ bonds ]\r
+; ai aj funct c0 c1 c2 c3\r
+ 1 2 1 \r
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+\r
+[ pairs ]\r
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+\r
+[ dihedrals ]\r
+; ai aj ak al funct c0 c1 c2 c3\r
+ 5 22 20 21 4 \r
+ 20 24 22 23 4 \r
+ 24 46 44 45 4 \r
+ 32 37 35 36 4 \r
+ 35 38 37 41 4 \r
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+ 73 77 75 76 4 \r
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+ 173 177 175 176 4 \r
+ 175 179 177 178 4 \r
+ 177 181 179 180 4 \r
+\r
+[ orientation_restraints ]\r
+; ai aj type exp. label alpha const. obs. weight\r
+; Hz nm^3 Hz Hz^-2\r
+\r
+ 46 47 1 1 1 3 6.083 1.1 1.0\r
+ 61 62 1 1 2 3 6.083 -0.4 1.0\r
+ 75 76 1 1 3 3 6.083 0.7 1.0\r
+ 94 95 1 1 4 3 6.083 2.0 1.0\r
+ 116 117 1 1 5 3 6.083 -0.1 1.0\r
+ 128 129 1 1 6 3 6.083 -0.1 1.0\r
+ 139 140 1 1 7 3 6.083 2.4 1.0\r
+ 146 147 1 1 8 3 6.083 -0.3 1.0\r
+ 165 166 1 1 9 3 6.083 -0.7 1.0\r
+\r
+; Include water topology\r
+#include "amber99sb-ildn.ff/tip3p.itp"\r
+\r
+#ifdef POSRES_WATER\r
+; Position restraint for each water oxygen\r
+[ position_restraints ]\r
+; i funct fcx fcy fcz\r
+ 1 1 1000 1000 1000\r
+#endif\r
+\r
+; Include topology for ions\r
+#include "amber99sb-ildn.ff/ions.itp"\r
+\r
+[ system ]\r
+; Name\r
+GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1; 3 SUBUNIT in water\r
+\r
+[ molecules ]\r
+; Compound #mols\r
+Protein_chain_A 1\r
+SOL 10\r
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff