[gmx-users] Re:provide opt way to perform simulation for protein and peptide -reg

venkatesh s svenkateshbioinformatics at gmail.com
Fri Sep 28 19:03:11 CEST 2012

Respected gromacs Users,
                                   I want perform protein (only one chain)
+ peptide (five amino acid) simulation to understand interaction between
both (can say what role are playing peptide with protein  )
so i did   like this pdb2gmx -f prot.pdb -o pro.gro -water tip3p -ignh
-chainsep ter
but in my .top file

[ molecules ]
; Compound        #mols
Protein_chain_A     1


1. its shows only one chain actually want show 2 chains, but  why it shows
1 chain ?

and may i want know above mentioned way of  doing protein+ peptide
molecular dynamics is correct?

2. other than that what else method or way is there perform protein peptide
MDS  kindly let me know?

Heartiest Thanks in Advance


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