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 time0.000 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
--
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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