[gmx-users] using vmd output for MDRUN

vivek sharma viveksharma.iitb at gmail.com
Thu Sep 18 09:26:45 CEST 2008

Hi There,

Following is the scenario I am trying for MDS
I am using vmd to modify the position of my molecule, and then output from
vmd is in .pdb format.
for .top file I have generated those files from pdb2gmx and edited them
manually as suggested in drug-enzyme tutorial by J E Kerrigan.

Now, I am in doubt weather I can use the .pdb from vmd & .top file for
running editconf and genbox followed by MDS ?

With Thanks,
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