Hi all,
I want to use MMPBSA to calculate binding energy formy protein conmplex,
but my result is very weird, since the van der Waals energy is quite high.
And an error message showed like this:
INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE, AND/OR
DIHED).
CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE
RELIABLE (check differences)!
The most common cause of this is inconsistent charge definitions across
topology files.
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 7952096.0436 1239353.8273
177050.5468
ANGLE 322047.5238 45147.3031
6449.6147
DIHED 11885.5386 1351.0769
193.0110
VDWAALS 255639253908530208.0000 1262730681757532416.0000
180390097393933216.0000
Then I tried to use ante-MMPBSA to generate compatible files for MMPBSA.
However, a error message showed like this:
Warning: there is an atom OXT in residue ASP237 which does not exist in the
model ASP!
This atom will not be created.
residue ASP237 has 13 atoms
N
H
CA
HA
CB
HB2
HB3
CG
OD1
OD2
C
O
OXT
model ASP has 12 atoms.
N
H
CA
HA
CB
HB2
HB3
CG
OD1
OD2
C
O
Warning: cannot find template for residue ASP in our library.
You will not be able to save prmtop for this molecule.
But ASP 237 is actually the terminal residue of my protein, there must be
an additional oxygen atom at the end of this residue. I did not quite get
this error message. Could anyone help solve this problem?
Thanks in advance for any help!
--
Shuyi Cao
Graduate student
Department of Medicinal chemistry and Pharmacognosy
College of Pharmacy
Univerisity of Illinois at Chicago
--
Shuyi Cao
Graduate student
Department of Medicinal chemistry and Pharmacognosy
College of Pharmacy
Univerisity of Illinois at Chicago
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Received on Mon Feb 06 2012 - 18:30:02 PST
