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
Regards
D.M
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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))....
>
>
>Now:
>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.
Mark
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