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

From: David A Case <>
Date: Wed, 20 May 2020 21:15:53 -0400

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.


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Received on Wed May 20 2020 - 18:30:02 PDT
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