Dmitry Lupyan wrote:
Dear GROMACS Users,
I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was
generated with NAMD (trajectory was converted to .trr w/VMD). The
g_hbond requires (i) a trajectory file, and (ii) a 'run input file'
(tpr/tpa/tpb). How do i generate this tpr/tpa/tpb file? Is there any
way I can use a plain PDB file for this?
For g_hbond, you need a .tpr file, which is the run input file for a GROMACS MD
simulation. You will need to go through the process of generating the topology
(pdb2gmx), building the corresponding system (genbox, genion), and build the
.tpr file with grompp.
Sounds like a good time to learn how to use GROMACS through tutorials :)
-Justin
-Dima
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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