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.",
"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[] = {
"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]",
"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]",
"#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",
"#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.",
"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",
"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",
"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",
"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",
"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[] = {
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",
"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",
"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]",
"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]",
"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]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] = {
"[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]",
"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",
"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",
"\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",
"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",
"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",
"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",
"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",
"\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"
};
"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.",
"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",
"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",
"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]",
"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, ",
"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]",
"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.",
"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",
"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