Re: [AMBER] Antechamber

From: David A Case <>
Date: Tue, 17 Sep 2013 07:36:33 -0400

On Tue, Sep 17, 2013, Jasim, Mahmood (Student) wrote:
> I have tried your suggestion and not solvate the system. The results
> were similar. I have attached the files for you to have a look please.

Unfortunately, what you sent is not enough to even understand the problem, let
alone to reproduce it. As I remember(?), you didn't have any LIG.pdb file in
your earlier post. If you are going to get help, you will need to post
(again) the exact commands you used, provide all the needed files, and
describe the problem in as much detail and specificity as you can. (That is,
don't just say, the "the pdb file I get from ambpdb is bad"; give an example
of exactly what you don't like about the result.)

What you seem to be doing is what we do every day with this code, so no one is
likely to say: "Oh, I recognize that problem". We have to be able to try to
reproduce the problem. You can help by trying to find a simple and small
example that illustrates it. Does this happen with every protein-ligand
complex you try, or just this particular one?


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Received on Tue Sep 17 2013 - 05:00:03 PDT
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