Re: AMBER: Non-standard amino acid residue

From: Sergey Samsonov <>
Date: Tue, 17 Jul 2007 14:30:14 +0200

Hi Francois,

thank you very much for your answer and suggestions!

FyD wrote:
> Quoting Sergey Samsonov <>:
> - Then, here you compare charge values for different residues (no
> information about their conformations !), and RESP vs AM1-BCC for
> different structures/conformations: You get higher differences which
> seem logical. I am not sure you can find empirical rules, and I am not
> sure such comparisons mean something...
That's what I mean exactly, to calculate the charges in AM1-BCC is not
the correct way to proceed with non-standard amino acid residues since
even the charges for the atoms of the same standard residue in the same
conformation will be really different if calculate in RESP and in
AM1-BCC, that is quite logical since the methods are principally different.

Trying RESP I faced another problem (it was already mentioned in the
mailing list but no really helpful answer was given,
When I try to produce the prepin file using antechamber by:

antechamber -i name.log -fi gout -o name.prepi -fo prepi -c resp -s 2

I receive the error:

Amber8 Module: resp
Amber8 Module: resp
Unit 3 Error on OPEN: qout
Cannot open charge file QOUT , exit

It seems that I should create ANTECHAMBER.ESP first? How can I deal with
>> Is there the way to use non-standard
>> amino acid residues within the protein without this charge problem?
> Electrostics is a key component of the FF energy.
> Concerning RESP and ESP charges & non-standard residues you might wish
> to have a look at the R.E.D. tutorial .
> You will find information about multi-orientation, multi-conformation
> and multi-molecule RESP fit for non-standard residues and their
> fragments (central and terminal ones).
Thank you for the useful link!

Thank you in advance and best regards,


> regards, Francois

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Received on Wed Jul 18 2007 - 06:07:42 PDT
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