On 4/28/2011 10:25 PM, Justin A. Lemkul wrote:
Ehud Schreiber wrote:
Dear Gromacs users,
I wish to convert PDB files to gromacs format while specifying the
topology;
That is not the role of pdb2gmx. pdb2gmx generates a topology that
matches a configuration (which could be in one of many file formats),
and (as a side effect) produces a "cleaned up" version of that
configuration (which again could be in one of many file formats).
If you already have your configuration and a .top file that has one or
more [moleculetype] sections that match the molecules present in your
configuration, you do not need pdb2gmx.
Perhaps this will help you reconsider whether your workflow is appropriate.
Mark
however, in the pdb2gmx program, a .top file can only be an output,
not an input.
The need arises as I have an NMR PDB structure (including hydrogens)
which I rather violently perturb into multiple PDB structures using
some non-gromacs means. When I convert those structures to .gro using
pdb2gmx, sometimes the protonation state of Histidine is guessed
incorrectly by the program (the hydrogen moves between HD1 and HE2).
If the atoms are properly named, I don't see how this is possible,
unless you're using the -ignh option. If the atomic coordinates are
severely skewed, you should at least get a warning about long bonds.
Does anybody have a suggestion what can I do? I need the process to
be automatic and so can’t use the interactive -his option.
So is the .top the same in all cases, and you're just altering
coordinates? If so, pdb2gmx is not necessary at all. Just use the
.top you want in conjunction with any of the .pdb files. But perhaps
I've missed the point. There is definitely no way to input a .top
into pdb2gmx since its principal function is to produce such a file.
-Justin
Thanks,
Ehud.
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