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

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 20 14:08:16 CEST 2010

It seems that my messages still are not getting through.  I'll try again to post 
this today, apologies if you're getting multiple...

Johannes Beck wrote:
> Dear Justin, dear all,
> thank you for your reply.
> Running protonate without defining an index file via -n is indeed 
> possible, but when the groups are to be chosen after calling protonate, 
> only a group named Protein that contains 82 residues was offered, but no 
> group containing 124 residues, as I wished to get for the protonated 
> molecule:
> ------------------
>  > protonate -s 65300.gro -f md.xtc -o md_protonated.xtc

That is exactly what you want - to protonate your protein, which currently has
82 atoms.  I have no idea about what the help information is talking about
(probably a more advanced application), but as for doing a simple protonation
like this one, your command is correct.


> Is the trajectory I now received (md_protonated.xtc) properly 
> protonated? How could I check this? For application of g_dist on this 

Use gmxcheck.  It will report the number of atoms in the trajectory.

> protonated trajectory, a run input file (.tpr) that corresponds to the 
> protonated state seems to be required. If the run input file from the 
> unprotonated MD trajectory is given as input in g_dist, g_dist fails and 
> suggests to use tpbconv in order to convert the original run input file 
> into a run input file for the protonated state. I wonder how I could use 
> tpbconv to do that?

tpbconv is only useful for making a subset of the original .tpr file, not for
adding atoms to it.  You can protonate the configuration in the .tpr file using
protonate, but the output can only be a coordinate file or trajectory, not a
.tpr file.  You will likely have to produce a new topology for your
now-protonated system that corresponds to the trajectory.



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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