AMBER Archive (2008)

Subject: Re: AMBER: Prepgen

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Aug 05 2008 - 10:50:00 CDT

Hello Everyone,
There is a bug with prepgen to do the charge correction. Please correct it
and recompile the program. To generate non-standard amino acid-like
residues, it is highly recommended to use residuegen, which can handle
single/multiple conformations and easier to use. If no charge correction was
needed or you used residuegen to generate non-standard residues, this bug
should not affect your results.

AmberTools-1.2 - Line 1114 of prepgen.c
Amber10 - Line 1112 of prepgen.c
Amber9 -Line 1043 of prepgen.c

Change "if (omitnum > 0 && charge >= 9990.)" to "if (omitnum > 0 && charge
<= 9990.)"

All the best

Junmei

On Wed, Jul 30, 2008 at 3:58 AM, Heikki Salo <hssalo_at_gmail.com> wrote:

> Dear Amber users,
>
> I have had exactly same problems as mentioned by Ojha. I tried to assign
> charges to my modified amino-acid but after using the prepgen, to remove the
> ACE and NME residues, the charge of the center amino-acid was not zero.
>
> I faced the same problem when I followed the antechamber tutorial 2. (on
> page http://amber.scripps.edu/antechamber/pro4.html). After using prepgen
> the charges did not match with the prepi file on the tutorial page. I
> noticed that the charges were not changed from the earlier ac file.
>
> I took a look at the source code of prepgen.c. I noticed that in the main
> program on line 1114 there is an following if statement:
> "if (omitnum > 0 && charge >= 9990.) {"
>
> After this follow the lines, where the charges of the atoms not in the omit
> list are calculated.
>
> If I got it right, the charge variable is the CHARGE on mainchain.dat file.
> Could there be a bug on this line, which could cause the problem. When would
> the charge variable get values over 9990? Please correct me if I intepreted
> the code completely wrong.
>
> The version of antechamber, which I am using is the one included in
> Ambertools-1.2.
>
> H. Salo
>
>
>
>

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