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

[Justin Lemkul]

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

-- 
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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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