[AMBER] Problem with parmed

From: Qinghua Liao <scorpio.liao.gmail.com>
Date: Wed, 17 May 2017 12:00:42 +0200

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!

All the best,

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Received on Wed May 17 2017 - 03:30:02 PDT
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