[gmx-users] RE: using vmd output for MDRUN

Vitaly Chaban chaban at univer.kharkov.ua
Thu Sep 18 11:53:38 CEST 2008

> 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 ?

Why not?

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698

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