[gmx-users] Trajectory protonation and inter proton distance calculation

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 18 19:21:45 CEST 2010

Johannes Beck wrote:
> Dear GROMACS users,
> I try to read inter-proton distances from an MD trajectory (GROMACS 
> 4.0.5, ffG53a6) of a peptide. As many distances referring to HAs, HBs 
> etc. are to be evaluated for comparison with NMR distance restraints, I 
> tried to use protonate to add all protons to the peptide trajectory (not 
> to the solvent which is DMSO).
> Both, protonation and evaluation of distances from the (putatively) 
> protonated trajectory brought me into some trouble.
> For protonate the GROMACS manual suggests the following:
> If an index file is specified, please note that the atom numbers should 
> correspond to the protonated state.
> However, if the number of atoms in the corresponding index file group is 
> equal to the total number of atoms in the protonated peptide (124 atoms 
> in my case), protonate fails as follows:

Does protonate work if you don't specify an index file at all?  If you're just 
trying to add protons to the protein and nothing else, then there is no need for 
an index group, since "Protein" is generated (and therefore can be chosen) by 



> the run input file used here (../inmd.tpr) is the one of the original MD 
> run. Unfortunately, I did not manage to make a matching run input file 
> using tpbconv. How could I do that?

Use protonate -s (with no -f flag, etc), as explained in the manual.



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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