[gmx-users] pdb2gmx with input topology
Mark.Abraham at anu.edu.au
Thu Apr 28 14:38:35 CEST 2011
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
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.
>> 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.
More information about the gromacs.org_gmx-users