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

From: Dawid das <>
Date: Wed, 20 May 2020 21:07:10 +0200

Hi David,

Thank you for your response. 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.

I tried
set x.66.N pert true
but it does not really work. I still get this error message as well as
incorrect number of bonds.

Best wishes,
Dawid Grabarek

śr., 20 maj 2020 o 19:43 David A Case <> napisał(a):

> On Wed, May 20, 2020, Dawid das wrote:
> >
> >When I use tleap to generate my parm file, I get an error
> >Bond: maximum coordination exceeded on A<N 7>
> > -- setting atoms pert=true overrides default limits
> How many atoms are bonded to this particular nitrogen? Are you sure
> that this odd coordination is what you expect?
> >
> >I have tried many times to use set like this:
> >set x.66.N pert=true
> >set default x.66.N pert=true
> I don't think tleap would ever use an "=" construct like this.
> You should try this:
> set x.66.N pert true
> (I'm just going by the output of "help set" inside tleap.)
> But I'm concerned that (even if it works) it may just be hiding
> something deeper that is wrong with your input.
> ....dac
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Received on Wed May 20 2020 - 12:30:02 PDT
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