[gmx-users] simulating dimer proteins
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
> 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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