Subject: autodock

From: Johanna Mazlo <[email-masked]>
Date: Sat, 7 Jul 2001 19:26:36 -0500 (CDT)

Hi CCL group,

I am a novice with modeling.  I am trying to dock an 8 residue peptide to
an antibody that will be used for rational mutagensis experiments.  I am
using autodock3.0. The peptide was produced using the biopolymer menu of
SYBYL, adding Essential_Only hydrogens, assigning KollUA partial charges,
and saving it as a mol2 file. I followed the "Getting Started" section of 
the manual.  When I run the deftors peptide.mol2, I receive several errors
in the .err file:  

REMARK *** ERROR 1 ***  Non-integral total charge (0.404) for residue AMN-
9!
REMARK *** ERROR 1 ***  Non-integral total charge (0.398) for residue PRO-
1!REMARK *** ERROR 1 ***  Non-integral total charge (0.992) for residue
ARG-   8!
REMARK *** ERROR 1 ***  Non-integral total charge (0.236) for residue AMN-
9!
REMARK *** ERROR 2 ***  Non-integral total charge (-1.034) for residue
CXL-  10!
REMARK *** ERROR 3 ***  Non-integral total charge (1.992) for whole
system!

I am not quite sure what to do next.  I would greatly appreciate your
advice.

Thank you

Johanna Mazlo
University of Nebraska
Lincoln, NE 68588-0304

[email-masked]