[gmx-users] gromacs trajctory mmpbsa

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 14 17:15:26 CEST 2008

Quoting jacopo.sgrignani at unifi.it:

> Dear gromacs user,
> I would like  to perform an MMPBSA calculation of a proetin ligand
> complex using a gromacs trajectory,  but this is the first time I try to
> do it so I have some questions.
> Did anybody use the Amber-MM-PBSA script with gromacs trajectory?
> I tried to transform the gromacs traj using VMD in a crd file but when i
> use the mm-pbsa script i can get only an error?

It's been a while since I've done anything with AMBER, but it might be worth
trying to use trjconv to output your trajectory frames as individual .pdb
files, then stitching them back together with ptraj (under AMBER) into an mdcrd
file.  I think this can be done, but no guarantees, and I certainly haven't done
it; I'm just thinking out loud.  It might be worthwhile to explore the AMBER
archive about doing this last step.


> Are there other solutions to perform this calculation without rerun the
> trejctory with Amber?
> I'm sorry if this is an old question, but i found only a message about
> this and It's quite old.
> Thanks a lot
> Jacopo
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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