Re: [AMBER] protein-protein complex dissociation

From: David A Case <>
Date: Thu, 16 Apr 2020 14:54:03 -0400

On Thu, Apr 16, 2020, Núbia Toman wrote:
>parm .top
>trajin .nc
>reference ref.rst
>strip :WAT,Na+,Cl- outprefix nowater
>center :1-330 origin
>image origin center
>rms reference :1-330
>rms reference :1-330.CA,C,N nofit out .dat

I'm rather lost here: if you are stripping waters and ions, none of the
image commands is likely to make much difference. How many molecules
are there in what is left?

Try leaving out the "center" and "image" commands: these may be undoing
all the good that "autoimage" did. It's also at least worth a try to
do the rms command before any imaging: again, the rms command might be
messing up what autoimage has already done.

Certainly for debugging, doing very simple cpptraj runs one at a time,
and looking at the outputs, may help localize the problem.

...good luck....dac

p.s.: if you ran your original simulation with iwrap=1, that may also be
a source of problems. Consider using the default value of 0 in future

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Received on Thu Apr 16 2020 - 12:00:02 PDT
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