[gmx-users] simulating dimer proteins

[Mark Abraham]

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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