AMBER: Antechamber/formatting question

From: Kara Di Giorgio <>
Date: Fri, 4 Feb 2005 15:05:18 -0800

I'm trying to model a minor groove binding agent bound to a 10-mer DNA
strand. I created the DNA in nucgen and am planning on creating a
custom unit consisting of the guanine/compound bound together and then
modifying the DNA-pdb to insert the custom unit instead of the guanine.
  As the DNA strand is symmetrical, one compound will be on each strand.
  (This seemed to be the method suggested in the tutorial "Simulating a
Solvated Protein that Contains Non-Standard Residues".)

1. Is this a reasonable approach to take? Is there another way to do
this that is easier?

2. I'm trying to create the custom unit using antechamber. I have a
previous (very old) pdb file that has the guanine/compound already
covalently attached. I've tried to delete all other information from
the pdb and then run it through antechamber. It fails when trying to
assign bond types. I get the message:

Running: /usr/local/amber/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o

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

Running: /usr/local/amber/exe/atomtype -i ANTECHAMBER_AC.AC0 -o

and then it goes on and tries to run divcon where it fails due to no

I've check the connectivity. I've run the compound itself through
antechamber with no problems. I've increased MAXVASTATE in define.h to
4000 and recompiled bondtype.C with no luck. I don't know what to
change in APS.DAT.

Any suggestions?

Thank you,

Kara Di Giorgio
University of the Pacific

p.s. I'm running on a MacG4 PowerBook through an X11 terminal window

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Received on Fri Feb 04 2005 - 23:52:59 PST
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