From 19d6d4f0e182196e87fe3b83b97360dc22eae811 Mon Sep 17 00:00:00 2001 From: "Justin A. Lemkul" Date: Wed, 6 Apr 2011 08:02:38 -0400 Subject: [PATCH] Added documentation about proper use of pdb2gmx -ter. --- src/kernel/pdb2gmx.c | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/src/kernel/pdb2gmx.c b/src/kernel/pdb2gmx.c index 8c8034a0a3..0f0ab36576 100644 --- a/src/kernel/pdb2gmx.c +++ b/src/kernel/pdb2gmx.c @@ -954,7 +954,7 @@ int main(int argc, char *argv[]) "[PAR]", "[TT]pdb2gmx[tt] will search for force fields by looking for", "a [TT]forcefield.itp[tt] file in subdirectories [TT].ff[tt]", - "of the current working directory and of the Gromacs library directory", + "of the current working directory and of the GROMACS library directory", "as inferred from the path of the binary or the [TT]GMXLIB[tt] environment", "variable.", "By default the forcefield selection is interactive,", @@ -965,7 +965,7 @@ int main(int argc, char *argv[]) "After choosing a force field, all files will be read only from", "the corresponding force field directory.", "If you want to modify or add a residue types, you can copy the force", - "field directory from the Gromacs library directory to your current", + "field directory from the GROMACS library directory to your current", "working directory. If you want to add new protein residue types,", "you will need to modify [TT]residuetypes.dat[tt] in the library directory", "or copy the whole library directory to a local directory and set", @@ -981,17 +981,22 @@ int main(int argc, char *argv[]) "The program has limited intelligence, it reads a number of database", "files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),", "if necessary this can be done manually. The program can prompt the", - "user to select which kind of LYS, ASP, GLU, CYS or HIS residue she", - "wants. For LYS the choice is between neutral (two protons on NZ) or", - "protonated (three protons, default), for ASP and GLU unprotonated", - "(default) or protonated, for HIS the proton can be either on ND1,", + "user to select which kind of LYS, ASP, GLU, CYS or HIS residue is", + "desired. For Lys the choice is between neutral (two protons on NZ) or", + "protonated (three protons, default), for Asp and Glu unprotonated", + "(default) or protonated, for His the proton can be either on ND1,", "on NE2 or on both. By default these selections are done automatically.", "For His, this is based on an optimal hydrogen bonding", "conformation. Hydrogen bonds are defined based on a simple geometric", "criterion, specified by the maximum hydrogen-donor-acceptor angle", "and donor-acceptor distance, which are set by [TT]-angle[tt] and", "[TT]-dist[tt] respectively.[PAR]", - + + "The protonation state of N- and C-termini can be chosen interactively", + "with the [TT]-ter[tt] flag. Default termini are ionized (NH3+ and COO-),", + "respectively. Some force fields support zwitterionic forms of isolated", + "amino acids, but for polypeptides these options should NOT be selected.[PAR]", + "The separation of chains is not entirely trivial since the markup", "in user-generated PDB files frequently varies and sometimes it", "is desirable to merge entries across a TER record, for instance", -- 2.11.4.GIT