Re: [AMBER] Problem with parmed

From: Jason Swails <>
Date: Wed, 17 May 2017 07:17:00 -0400

On Wed, May 17, 2017 at 6:00 AM, Qinghua Liao <>

> 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:

Here are the API docs:

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


Jason M. Swails
AMBER mailing list
Received on Wed May 17 2017 - 04:30:02 PDT
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