On 16/06/2012 5:03 PM, delara aghaie wrote:
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?
You don't need a .gro file:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#section_1.
You need a coordinate file that matches the contents of the .top file.
Whether that is easy depends what you did with pdb2gmx.
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??
-------------------------
See pdb2gmx -h for how to do chain management - but if you can run
pdb2gmx on your multi-chain coordinate file, then you don't need to get
involved with the contents of
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains
Mark
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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