[gmx-users] Re:provide opt way to perform simulation for protein and peptide -reg
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
but in my .top file
[ molecules ]
; Compound #mols
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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