[gmx-users] pdb2gmx with input topology

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 28 14:25:36 CEST 2011

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.


> Thanks,
> Ehud.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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