[gmx-users] simulating dimer proteins

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jun 16 09:43:10 CEST 2012

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: 
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 


> 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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