Dear Amber users,
I am trying to do MCPB calculation for model the ion in the protein I am
studying. Following the tutorial (
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm) I have
generated the gaussian input files (.com) for side chain model for geometry
optimization and large model for MK RESP charge calculation.
Unfortunately,both the geometry optimization and the MK RESP charge
calculation with Gaussian 09 failed with the following error message.
1. The geometry optimization with side chain model failed with the error
message -
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Using GEDIIS/GDIIS optimizer.
Bend failed for angle 50 - 58 - 57
Tors failed for dihedral 11 - 50 - 58 - 57
Tors failed for dihedral 12 - 50 - 58 - 57
Tors failed for dihedral 23 - 50 - 58 - 57
Tors failed for dihedral 46 - 50 - 58 - 57
Tors failed for dihedral 56 - 57 - 58 - 50
Tors failed for dihedral 59 - 57 - 58 - 50
Tors failed for dihedral 60 - 57 - 58 - 50
FormBX had a problem.
Error termination via Lnk1e in
/usr/local/Cluster-Apps/gaussian/g09/l103.exe at Fri Feb 26 05:30:24 2016.
Job cpu time: 0 days 20 hours 52 minutes 0.8 seconds.
File lengths (MBytes): RWF= 207 Int= 0 D2E= 0 Chk= 25
Scr= 1
2. The MK RESP charge calculation with large model failed with following
error message -
***********************************************************************************************
93 1 1.20
94 25 0.00
GetVDW: no radius for atom 94 atomic number 25.
Error termination via Lnk1e in
/usr/local/Cluster-Apps/gaussian/g09/l602.exe at Fri Feb 26 04:22:16 2016.
Job cpu time: 5 days 5 hours 40 minutes 37.2 seconds.
File lengths (MBytes): RWF= 623 Int= 0 D2E= 0 Chk= 69
Scr= 1
*****************************************************************************************************
In this case, I have seen that the .com file have the radius of Mn ion
mentioned in it and the log file shows the Gaussian 09 successfully read
the radius for Mn ion.
A part of the log file shows...
Merz-Kollman atomic radii used.
Read replacement radii for each type of atom:
Rad(25) = 1.467000000000D+00
It will be of great help if anybody help me to figure out what went wrong
in both Gaussian calculations.
Many thanks in advance
Anu
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Received on Fri Feb 26 2016 - 03:30:04 PST
