[gmx-users] simulating dimer proteins

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 10:00:34 CEST 2012

Dear Mark
Thanks for your complete explanation. 

Now I have a question about adding ions to this system. I see the chain A has qtot=-1 and also the chain B has qtot=-1.

Now If I add two positive ions using the genion command, is it ok to make my system neutral?
I mean is it the same as the case where two negative ions were on a single protein?
Thanks again

From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 12:15
Subject: Re: [gmx-users] simulating dimer proteins

On 16/06/2012 5:31 PM, delara aghaie wrote: 
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))....
>Can I use these files to continue the simulations or again it is necessary to follow the procedure explained in multiple chains gromacs???
By definition of pdb2gmx function, you now have a topology and a
    coordinate file that matches. That is the minimum requirement for
    grompp to succeed later. grompp doesn't care about some aspects of
    atom numbering - including your observation above.


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