Re: [AMBER] How to use set pert=true

From: Dawid das <>
Date: Fri, 22 May 2020 16:34:35 +0200

Yes, I am familiar with this tutorial. Generally speaking, my procedure
works for all
modified amino acids (chromophores) but RFP. I checked the definition of
atoms, the
structure of lib and parm as well as bonding information a few times and I
still can't
figure out what the source of problem is.

Best wishes,
Dawid Grabarek

czw., 21 maj 2020 o 03:16 David A Case <> napisaƂ(a):

> On Wed, May 20, 2020, Dawid das wrote:
> >
> >This is nitrogen of acylimine group C=N-C=O, so it is connected to two
> >atoms only. It is part of a red fluorescent protein chromophore (C=N
> >part) and is connected to the preceding amino acid residue. In fact, when
> >I check the number of bonds in my parm file, I get a wrong number of both
> >heavy atom - heavy atom as well as heavy atom - hydrogen atom bonds.
> Sounds like tleap is telling you something that is good to know: that
> some step in creating the modfied amino acid (aka chromophore) has gone
> awry, and you are getting the wrong list of bonds.
> If you by chance haven't seen it, there is a tutorial on GFP, which
> might help.
> ....dac
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Received on Fri May 22 2020 - 08:00:03 PDT
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