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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