[gmx-users] simulating dimer proteins

[delara aghaie]

Dear Gromacs Users

Running pdb2gmx on a pdb file containing a dimer protein, I used option (( chainsep id_or_ter)))
This resulted in separated topologies for each chain and separated posre files. Also in the .gro file, the aminoacides of the second chain started from number 1. (Without this option the second chain aminoacides will receive numbers in continuation of numbers of first chain))....

Now:
Can I use these files to continue the simulations or again it is necessary to follow the procedure explained in multiple chains gromacs???

Thanks
Regards
D.M




________________________________
 From: delara aghaie <d_aghaie at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 11:33
Subject: Re: [gmx-users] simulating dimer proteins
 

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.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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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