Ehud Schreiber wrote:
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).
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.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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