[gmx-users] Re:provide opt way to perform simulation for protein and peptide -reg
jalemkul at vt.edu
Fri Sep 28 19:11:40 CEST 2012
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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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