[gmx-users] pdb2gmx with input topology

[Ehud Schreiber]

Dear Gromacs users,

 

I wish to convert PDB files to gromacs format while specifying the
topology; 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).

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. 

 

Thanks,

Ehud.

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110428/a412cf39/attachment.html>