CCL:G: Error performing ONIOM calculation in MM part
From: "Mahmoud A. A. Ibrahim"
<m.ibrahim1982[*]yahoo.com>
Subject: CCL:G: Error performing ONIOM calculation in MM part
Date: Wed, 29 Jul 2009 08:25:26 -0700 (PDT)
In order to know which parameters you are missing for
your compound (Protein/ligand), you should use antechamber program and parameter
check program (parmchk), these two programs are shipped with
AMBER. Antechamber to assign the atom types, and parmchk to find the missing
ones, Antechamber can be used in cooporation with gaff. Note: Gaussian
versions upto 03 uses parm94 force field, so YOU HAVE TO define parm95 in your
command in parmchk (-p parm95). Sincerely; M. Ibrahim
Mahmoud A. A. Ibrahim
Current Address
School of Chemistry, University of Manchester, Oxford
Road, Manchester, M13 9PL, United
Kingdom. Mahmoud.Ibrahim-2/a\postgrad.manchester.ac.uk
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Address
Chemistry Department, Faculty of Science,
Minia University, Minia 61519,Egypt.
M.Ibrahim1982/a\yahoo.com Mobile Phone No.: +20102554083
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--- On Tue, 7/21/09,
Beatriz C Ramirez bea_ucv__yahoo.com
<owner-chemistry/a\ccl.net> wrote:
From: Beatriz C Ramirez bea_ucv__yahoo.com
<owner-chemistry/a\ccl.net> Subject: CCL:G: Error performing ONIOM
calculation in MM part To: "Ibrahim, Mahmoud A. A. "
<m.ibrahim1982/a\yahoo.com> Date: Tuesday, July 21, 2009, 5:25
AM
Sent to CCL by: "Beatriz C Ramirez"
[bea_ucv _ yahoo.com] Im trying to perform an ONIOM calculation pm3:amber
with a .pdb structure from an enzymatic intermediate. I added the amber atom
types and the charges for the MM atoms but I still got this error.
Angle
bend undefined between
atoms 71 74 75 Angle bend
undefined between
atoms 72 71 74 Angle bend
undefined between
atoms 73 74 75 Angle bend
undefined between
atoms 74 75 76 Angle bend
undefined between atoms 141 8 144 MM function not
complete Error termination via Lnk1e in
C:\G03W\l101.exe at Mon Jul 20 19:27:33 2009. Job cpu time: 0
days 0 hours 0 minutes 5.0 seconds. File lengths
(MBytes): RWF= 7 Int= 0 D2E=
0 Chk= 1 Scr=
1
Apparently I have to specify some angles, but I dont know how to do it,
or how to edit this AMBER parameters, such as impropers or dihedrals for this
molecule.
I'll appreacite your help because im running out of
ideas Beatriz Ramirez
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