AMBER Archive (2007)

Subject: Re: AMBER: Non-standard amino acid residue

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jul 17 2007 - 08:41:57 CDT

Quoting Sergey Samsonov <sergeys_at_biotec.tu-dresden.de>:

> 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.

Personnally, I work with RESP charges and even with this approach
there are many pitfalls... Since it is already difficult to reproduce
published RESP charge values, I am not surprised the differences are
even higher with AM1-BCC.

> Trying RESP I faced another problem (it was already mentioned in the
> mailing list but no really helpful answer was given,
> http://structbio.vanderbilt.edu/archives/amber-archive/2005/0324.php).
> 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
> Unit 10 Error on OPEN: ANTECHAMBER.ESP
> 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 that?

Sorry, I use R.E.D. with
multi-molecules/multi-conformations/multi-orientations RESP fit. This
allows to generate (i)multi-orientations: highly reproducible RESP
charge values, (ii)multi-conformations: general/high quality charge
values required in MD simulation and (iii)multi-molecules: to generate
charge values for any types of molecular fragments.

Concerning your problem, a quick google search from
http://amber.scripps.edu/, & you get a problem really similar to yours
"Unit 10 Error on OPEN: ANTECHAMBER.ESP":

http://amber.ch.ic.ac.uk/archive/200501/0263.html
and @ http://amber.ch.ic.ac.uk/archive/200501/0285.html, you get an answer.

regards, Francois

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