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

Justin Lemkul 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
> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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