Re: [AMBER] antechamber issue and parameters for heme of cyp3a4

From: Jio M <>
Date: Sat, 19 Jun 2010 11:03:27 -0700 (PDT)


1) Antechamber cannot handle Fe or other metals(somebody pls correct me if I m wrong)

2) For parameters you can follow some publications but note the units they are using or in this link

3) for water I dont know

--- On Sat, 6/19/10, vaibhav dixit <> wrote:

From: vaibhav dixit <>
Subject: [AMBER] antechamber issue and parameters for heme of cyp3a4
To: "AMBER Mailing List" <>
Date: Saturday, June 19, 2010, 5:00 AM

Dear Amber community members,
Thanks a lot for your suggestions and comments earlier.

Using the advanced tutorial for non-standard residues, I'm trying to prepare
library for heme residue.
 I'm using 2jod.pdb and considering Fe-porphyrin and one co-ordinated water
molecule as part of the residue CYS442. Is this a good approximation?

I have calculated esp potential for the same using Gaussian03 for the
crystal structure geometry.
But the antechamber is not working properly with the following error.
The lib file generated (cyx.lib.txt) and non-standard residue with Heme
cystein and water (heme_cyx_w.pdb) are attached.
Please find time and see if you can suggest some solution for the same.
Is there another approach to deal with the same issue of handling Heme
residues for performing MD studies on CYPs.

Waiting for your comments and thanks in advance...

The error with antechamber:
[vaibhav.localhost 1tqn]$ antechamber -i heme_cys_w.gout -fi gout -o
heme_cys_w.prep -fo prepi -c resp

For atom[7]:Fe1, the best APS is not zero, bonds involved by this atom are

Warning: the assigned bond types may be wrong, 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
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly
increase the computer time
Error: cannot run "/home/vaibhav/software/amber10/bin/bondtype -j full -i
judgebondtype() of antechamber.c properly, exit

With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
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