[gmx-users] two peptides in same water box

Mark Abraham 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 ]

mypeptide   2
SOL         23425


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