Re: [AMBER] Targeted MD

From: Carlos Simmerling <>
Date: Thu, 25 Apr 2019 08:01:37 -0400

Can you be a little more specific with your info? Do you have the 2
conformations of the protein? One will be the initial structure, one will
be used for the target structure (refc). Both must be run through leap and
have the same number of atoms. They must correspond to exactly the same
system in different coordinates.

If you think you did this and it didn't work, please look more closely at
the 2 leap.log files (it's best if you build the 2 conformations in
separate directories so that you have separate leap.log files).

On Thu, Apr 25, 2019, 4:08 AM Elena Gomez <> wrote:

> Dear Amber Users,
> I'm trying to do a targeted MD between two protein conformations but I
> don't know how to create the refc file with the final conformation. Could
> anyone please help me? I tried it building the file from inpcrd file but
> when I run sanders this error appears:
> FATAL: NATOM mismatch in constraint coord and topology files
> Thank you.
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Received on Thu Apr 25 2019 - 05:30:02 PDT
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