On 9/28/12 1:03 PM, venkatesh s wrote:
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
Question
1. its shows only one chain actually want show 2 chains, but why it shows
1 chain ?
The result implies that the two chains are not properly separated by a TER line.
and may i want know above mentioned way of doing protein+ peptide
molecular dynamics is correct?
What you're doing is generating a topology; you're not running MD yet. The
command line is syntactically correct, but there is something wrong with the
input .pdb file, otherwise you would have two chains written to the topology.
2. other than that what else method or way is there perform protein peptide
MDS kindly let me know?
This question doesn't make sense to me. Running MD on a complex is certainly a
viable way to study the interactions, but you're not even close to doing that
yet since your topology is not yet correct.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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