AMBER Archive (2007)

Subject: AMBER: Antechamber--Boron Parameters

From: brmeher_at_iitg.ernet.in
Date: Mon Jun 25 2007 - 05:04:30 CDT

Dear Amber Users,

I was trying to set the parameters for my ligand (containig a Boron
atom)
 for a protein-ligand system. When I run the antechamber
with the command   
$AMBERHOME/exe/antechamber -i
5401_H_attch.pdb -fi pdb -o 5401.prepin -fo
prepi -c bcc -s
2     

I got a message like

Cannot successfully assign bond type for this molecule, please:
(1)
double check the structure (the connectivity) and/or
(2)adjust atom
valence penalty parameters in APS.DAT, and/or
(3)increase MAXVASTATE
in define.h and recompile bondtype.C

When I checked the APS.dat
file , I didn't find any defined valence state for
Boron atom. So I
am in worry whether due to this problem I am getting the
error
message or something else.

Also I tried to find out the
parameters for Boron from the Amber archive,
but failed to get any
messages.

Can anybody please help me in this regard.
Any suggestions will be highly appreciated.

regards
B R
Meher

Biswa Ranjan Meher
Research Scholar,
IIT Guwahati,
Assam-781039

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu