[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
> > 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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