On Wed, May 17, 2017 at 6:00 AM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:
> Dear Amber users,
>
> I have an enzyme, which is a dimer. First, I built the system with
> tleap, I got the prmtop and inpcrd files.
> Then I used parmed to convert the prmtop and inpcrd into top and gro
> files in Gromacs format.
> As the two monomers are identical, only one monomer was indexed in the
> topology file while the other monomer was
> treated as a copy of the first monomer. Normally, it works fine. But
> now, I want to apply some distance restraints between
> atoms from the two monomers, respectively. Thus, what I want is that
> parmed can index the whole dimer including substrates
> in the top file. Could some one give me some tips how to do it with
> parmed? Thanks a lot!
>
​There is an argument called "combine" in the ​GromacsTopologyFile object
that will combine any set of adjacent "moleculetypes" into the same
"moleculetype" (which I believe is precisely what you are looking for
here). See a description of that here:
http://parmed.github.io/ParmEd/html/gromacs.html#writing-gromacs-topology-files
Here are the API docs:
http://parmed.github.io/ParmEd/html/gromacsobj/parmed.gromacs.GromacsTopologyFile.html#parmed.gromacs.GromacsTopologyFile.write
Shortcut: add the argument combine='all' to the Gromacs write() function
call to do what you want (that is, if I understand what it is you want to
do).
HTH,
Jason
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 17 2017 - 04:30:02 PDT
