On 5/14/12 8:42 AM, Steven Neumann wrote:
Dear Gmx Users,
i run the implicit simulation with virtual sites on the hydrogen of my protein.
Now I want to extract coordinates and run another simulation (in explicit
solvent). Is there any way to remove those virtual sites from my gro file as VMD
write the file using atoms not recognized by pdb2gmx obviously? Please, help!
Virtual sites have rather obvious names that lend themselves well to being
grepped out, i.e.:
grep -v "M[CN]" conf.gro > conf_clean.gro
Adjust the number of atoms in conf_clean.gro and proceed.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
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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