[gmx-users] How to protonate a gmx trajectory?

[Justin A. Lemkul]

Yun Shi wrote:
> Hi there,
> 
> I am using GROMACS4.5.4 and the GROMOS 53A6 united-atom force field to do MD with my protein-ligand system.
> 
> I was trying to add aliphatic hydrogens to the .gro and .trr or .xtc trajectory file with g_protonate, but the Fatal error was:
> 
> Library file in current dir nor  not found ffgmx2in defalt directories.
> 
> Then re-name the directory in ../share/top/gmx2.ff to ffgmx2, and this time g_protonate seems to be able to find those .hdb files. But another error follows as:
> 
> Reading frames from gro file 'Protein in water', 66743 atoms.
> Reading frame       0 time    0.000   Opening force field file ffgmx2/aminoacids.hdb
> Opening force field file ffgmx2/atomtypes.atp
> Atomtype 1
> Opening force field file ffgmx2/aminoacids.n.tdb
> Opening force field file ffgmx2/aminoacids.c.tdb
> Segmentation fault
> 
> 
> I searched for 'Segmentation fault', nothing relevant to g_protonate came up.
> 

A segmentation fault is a generic memory error that can be produced by any program.

> So I wonder if anyone could kindly help me out? Or is there an easy alternative way to protonate the trajectory file?
> 

The g_protonate program is currently nonfunctional.  I have made a small fix in 
the release-4-5-patches branch, but the result is that the program can only 
handle .pdb files and nothing else.

There is an outstanding issue that awaits a real resolution:

http://redmine.gromacs.org/issues/589

In the meantime, I guess the only workaround is to generate .pdb files of each 
of your trajectory frames, then re-concatenate them as a new .xtc file.  That 
would be somewhat tedious, but should work.

-Justin

-- 
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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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