Carla Jamous wrote:
Hi everyone,
I'm using this command to extract my protein and my ligand from the
trajectory.
trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n
prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj
Before, I had a problem with residues of my protein showing at the other
end of the box, when I display my .xtc with VMD.
the "-pbc whole" fixed it.
However, now I have another issue: my ligand is at the other end of the
box. So please can anyone tell me what can I do to fix that and get a
reasonable RMSD value?
You may need several more iterations of trjconv (one rarely does the trick),
employing -pbc nojump, -pbc cluster, and/or -center. For protein-ligand
complexes, I have often found that the combination of:
trjconv -pbc mol -ur compact -center
(centering on "Protein")
does the trick. And it makes molecules whole, as well :) I think there are
also some breakdowns (documented somewhere in the list archive) when applying
-fit and -pbc in the same step. I believe it is recommended to fix PBC first,
then applying any sort of fitting in a separate, subsequent step.
-Justin
Thank you
Carla
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
