On 14/05/2012 10:42 PM, 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!
If your original pdb2gmx workflow with virtual sites was recorded in a
shell script you'd
a) have a record for when you go to write up, and
b) be able to do this change easily.
As it is, a few minutes with a text editor would probably work for small
systems. Alternatively
grep -v MCH3 in.gro > temp.gro
will remove all of the lines for virtual sites named MCH3. Do that for
each type of virtual site. Adjust the count of atoms at the top of the
.gro file suitably at the end.
Mark
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