Dear Mark
Many thanks for your response.
Now A question:
I have read multiple chains section in gromacs website. It says take a
structure file with single chain and use pdb2gmx on it. In the resulting .top
file at the end of file, we see
{molecule}
protein
we should change the protein number to the number of identical chains. and then
submit this .top with the coordinate file containing the same number of chains
as mentioned in .top file: (((I have the pdf format of structure for 2 chains,
How can I get the .gro file for them? as I have done pdb2gmax on a single
chain, I do not have a .gro file containing 2 chains. Should I separately do
pdb2gmax on this .top file to get .gro containing 2 chains?))))
--------------------
As a test, Once I did pdb2gmx on a source pdb file of 1RFB. As a result I have
.gro file which has putted the aminoacides of the second chain after the first
chain without separating them. (This does not show the protein as two separate
chains !! ). Also it gives .top files separately for each chain. Are these
results correct??
-------------------------
Regards
D.M
-
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Friday, 15 June 2012, 12:03
Subject: Re: [gmx-users] simulating dimer proteins
On 15/06/2012 3:56 PM, delara aghaie wrote:
Dear Gromacs users
>I want to compare some properties of two Interferons via MD
simulation.
>One comes with pdb ID : 1ITF. (It has 24 Models in single pdb
file, but each model with single chain.) I did pdb2gmx on this.
>
>The other is with pdb ID of : (1RFB). This has two chanis
>--------------------------------
>DBREF 1RFB A 1 119 UNP P07353 IFNG_BOVIN 24
142
>DBREF 1RFB B 1 119 UNP P07353 IFNG_BOVIN 24
142
>-------------------------------
>
>Now the question: Is it wise to select only chain A and do the
simulations on it in order to compare with the 1ITF, which has
one chain?.
>I have read about simulating multiple chains in manual. But I
think the comparison between a protein with single chain and the
other with two chains may not be correct. (I want to compare
gyration radiuses and secondary structures)
>
The number of chains is not really the issue - you want to compare
things that are comparable. If 1RFB contains a dimeric structure
that does the same job as the monomeric 1ITF then they might be
comparable.
I want to know if it is common to do MD on selected chain of a dimer?
>
It happens. Whether it makes scientific sense in your case is
something you have to address.
Mark
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