Re: [AMBER] Problem with parmed

From: Qinghua Liao <>
Date: Wed, 17 May 2017 13:23:59 +0200

Dear Jason,

Thanks so much for your information. Yeah, it is what I want.

All the best,

On 05/17/2017 01:17 PM, Jason Swails wrote:
> On Wed, May 17, 2017 at 6:00 AM, Qinghua Liao <>
> 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:
> 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
> do).
> HTH,
> Jason

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Received on Wed May 17 2017 - 04:30:03 PDT
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