a bit cleaner and more consistent.
"This program is essential for checking your run input file in case of",
"problems.[PAR]",
"The program can also preprocess a topology to help finding problems.",
- "Note that currently setting GMXLIB is the only way to customize",
+ "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
"directories used for searching include files.",
};
t_filenm fnm[] = {
"Note that the atom names are irrelevant for the simulation as",
"only the atom types are used for generating interaction parameters.[PAR]",
- "[TT]grompp[tt] uses a built-in preprocessor to resolve includes, macros ",
- "etcetera. The preprocessor supports the following keywords:[BR]",
+ "[TT]grompp[tt] uses a built-in preprocessor to resolve includes, macros, ",
+ "etc. The preprocessor supports the following keywords:[BR]",
"#ifdef VARIABLE[BR]",
"#ifndef VARIABLE[BR]",
"#else[BR]",
"#include \"filename\"[BR]",
"#include <filename>[BR]",
"The functioning of these statements in your topology may be modulated by",
- "using the following two flags in your [TT]mdp[tt] file:[BR]",
+ "using the following two flags in your [TT].mdp[tt] file:[BR]",
"define = -DVARIABLE1 -DVARIABLE2[BR]",
"include = -I/home/john/doe[BR]",
"For further information a C-programming textbook may help you out.",
"calling the dssp program. If you do not have the dssp program,",
"get it. [TT]do_dssp[tt] assumes that the dssp executable is",
"/usr/local/bin/dssp. If this is not the case, then you should",
- "set an environment variable [BB]DSSP[bb] pointing to the dssp",
+ "set an environment variable [TT]DSSP[tt] pointing to the dssp",
"executable, e.g.: [PAR]",
"[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
"The structure assignment for each residue and time is written to an",
"they should be included within the correct [TT][ moleculetype ][tt]",
"block in the topology. Since the atom numbers in every moleculetype",
"in the topology start at 1 and the numbers in the input file for",
- "genpr number consecutively from 1, genpr will only produce a useful",
- "file for the first molecule.[PAR]",
+ "[TT]genrestr[tt] number consecutively from 1, [TT]genrestr[tt] will only",
+ "produce a useful file for the first molecule.[PAR]",
"The [TT]-of[tt] option produces an index file that can be used for",
"freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
"With the [TT]-disre[tt] option, half a matrix of distance restraints",
int gmx_helix(int argc,char *argv[])
{
const char *desc[] = {
- "[TT]g_helix[tt] computes all kind of helix properties. First, the peptide",
- "is checked to find the longest helical part. This is determined by",
- "Hydrogen bonds and Phi/Psi angles.",
+ "[TT]g_helix[tt] computes all kinds of helix properties. First, the peptide",
+ "is checked to find the longest helical part, as determined by",
+ "hydrogen bonds and Phi/Psi angles.",
"That bit is fitted",
"to an ideal helix around the Z-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file [TT]radius.xvg[tt]). This is merely the",
- "RMS deviation in two dimensions for all Calpha atoms.",
+ "RMS deviation in two dimensions for all C-alpha atoms.",
"it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file [TT]twist.xvg[tt]). The average helical angle per",
"number of helical residues (see below).[BR]",
"[BB]5.[bb] Number of helical residues (file [TT]n-ahx.xvg[tt]). The title says",
"it all.[BR]",
- "[BB]6.[bb] Helix Dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
- "[BB]7.[bb] RMS deviation from ideal helix, calculated for the Calpha",
+ "[BB]6.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
+ "[BB]7.[bb] RMS deviation from ideal helix, calculated for the C-alpha",
"atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
- "[BB]8.[bb] Average Calpha-Calpha dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
+ "[BB]8.[bb] Average C-alpha - C-alpha dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
"[BB]9.[bb] Average Phi and Psi angles (file [TT]phipsi.xvg[tt]).[BR]",
- "[BB]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]",
+ "[BB]10.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
"[PAR]"
};
static const char *ppp[efhNR+2] = {
"directions require a second index group of the same size, containing",
"the heavy atom in each residue that should represent the sidechain.[PAR]",
"Note that this program does not do any fitting of structures.[PAR]",
- "We need four Calpha coordinates to define the local direction of the helix",
+ "We need four C-alpha coordinates to define the local direction of the helix",
"axis.[PAR]",
"The tilt/rotation is calculated from Euler rotations, where we define",
"the helix axis as the local X axis, the residues/CA-vector as Y, and the",
"\n",
"SHORT METHOD DESCRIPTION\n",
"------------------------\n",
- "1. The protein is resized around its center of mass by a factor -xy in the xy-plane",
- "(the membrane plane) and a factor -z in the z-direction (if the size of the",
+ "1. The protein is resized around its center of mass by a factor [TT]-xy[tt] in the xy-plane",
+ "(the membrane plane) and a factor [TT]-z[tt] in the z-direction (if the size of the",
"protein in the z-direction is the same or smaller than the width of the membrane, a",
- "-z value larger than 1 can prevent that the protein will be enveloped by the lipids).\n",
+ "[TT]-z[tt] value larger than 1 can prevent that the protein will be enveloped by the lipids).\n",
"2. All lipid and solvent molecules overlapping with the resized protein are removed. All",
- "intraprotein interactions are turned off to prevent numerical issues for small values of -xy",
- " or -z\n",
+ "intraprotein interactions are turned off to prevent numerical issues for small values of [TT]-xy[tt]",
+ " or [TT]-z[tt]\n",
"3. One md step is performed.\n",
- "4. The resize factor (-xy or -z) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the",
+ "4. The resize factor ([TT]-xy[tt] or [TT]-z[tt]) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the",
"protein is resized again around its center of mass. The resize factor for the xy-plane",
- "is incremented first. The resize factor for the z-direction is not changed until the -xy factor",
- "is 1 (thus after -nxy iteration).\n",
- "5. Repeat step 3 and 4 until the protein reaches its original size (-nxy + -nz iterations).\n",
- "For a more extensive method descrition see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n",
+ "is incremented first. The resize factor for the z-direction is not changed until the [TT]-xy[tt] factor",
+ "is 1 (thus after [TT]-nxy[tt] iterations).\n",
+ "5. Repeat step 3 and 4 until the protein reaches its original size ([TT]-nxy[tt] + [TT]-nz[tt] iterations).\n",
+ "For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n",
"\n",
"NOTE\n----\n",
" - Protein can be any molecule you want to insert in the membrane.\n",
" - It is recommended to perform a short equilibration run after the embedding",
- "(see Wolf et al, J Comp Chem 31 (2010) 2169-2174, to re-equilibrate the membrane. Clearly",
+ "(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly",
"protein equilibration might require longer.\n",
"\n"
};
"manual chapter 1 for details. The result includes subtracting a harmonic",
"degree of freedom at the given temperature.",
"The total correction is printed on the terminal screen.",
- "The recommended way of getting the corrections out is:",
- "g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr]",
- "The constr should be used when bond constraints were used during the",
+ "The recommended way of getting the corrections out is:[PAR]",
+ "[TT]g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]",
+ "The [TT]-constr[tt] option should be used when bond constraints were used during the",
"simulation [BB]for all the covalent bonds[bb]. If this is not the case",
- "you need to analyse the quant_corr.xvg file yourself.[PAR]",
- "To make things more flexible, the program can also take vsites into account",
+ "you need to analyse the [TT]quant_corr.xvg[tt] file yourself.[PAR]",
+ "To make things more flexible, the program can also take virtual sites into account",
"when computing quantum corrections. When selecting [TT]-constr[tt] and",
- "[TT]-qc[tt] the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.",
- "Again, if you think you know it better, please check the eigenfreq.xvg",
+ "[TT]-qc[tt], the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.",
+ "Again, if you think you know it better, please check the [TT]eigenfreq.xvg[tt]",
"output."
};
"Option [TT]-mw[tt] controls whether mass weighting is done or not.",
"If you select the option (default) and ",
"supply a valid [TT].tpr[tt] file masses will be taken from there, ",
- "otherwise the masses will be deduced from the atommass.dat file in",
- "the GROMACS library directory. This is fine for proteins but not",
- "necessarily for other molecules. A default mass of 12.011 amu (Carbon)",
+ "otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
+ "[TT]GMXLIB[tt]. This is fine for proteins, but not",
+ "necessarily for other molecules. A default mass of 12.011 amu (carbon)",
"is assigned to unknown atoms. You can check whether this happend by",
"turning on the [TT]-debug[tt] flag and inspecting the log file.[PAR]",
"which has the advantage that no fit is needed like in standard RMS",
"deviation as computed by [TT]g_rms[tt].",
"The reference structure is taken from the structure file.",
- "The rmsd at time t is calculated as the rms",
+ "The RMSD at time t is calculated as the RMS",
"of the differences in distance between atom-pairs in the reference",
"structure and the structure at time t.[PAR]",
"[TT]g_rmsdist[tt] can also produce matrices of the rms distances, rms distances",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff