[gmx-users] two peptides in same water box
Mark.Abraham at anu.edu.au
Tue Mar 17 07:25:56 CET 2009
Bhawana Gupta wrote:
> Hello everyone,
> pls tell me that how should i do dimerization.
> i.e. i want to put two peptides in same water box, but i am not getting
> of how to do it.
Please make an effort to spell and punctuate like you're a professional
worth helping ;-)
One approach is to make an .itp file for the peptide (possibly via using
pdb2gmx on that peptide, and editing the resulting .top file in
consultation with Chapter 5 of the manual to create a suitable .itp
file). Generate your starting configuration for your pair of peptides.
Apply genbox and/or editconf to solvate. Construct a .top file whose
final [molecules] section resembles
[ molecules ]
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