[gmx-users] simulating dimer proteins

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jun 16 09:45:29 CEST 2012

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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120616/89396c7c/attachment.html>

More information about the gromacs.org_gmx-users mailing list