AMBER Archive (2008)

Subject: Re: AMBER: Prepgen

From: Heikki Salo (
Date: Wed Jul 30 2008 - 03:58:28 CDT

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 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

H. Salo

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