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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
