AMBER Archive (2009)

Subject: [AMBER] Conversion of Gaussian output file into mol2

From: megha bajaj (micro.megha_at_gmail.com)
Date: Wed Oct 28 2009 - 03:00:35 CDT

Dear all,

I am using Antechamber in Amber9.
Firstly i ran Gaussian03 for charge derivation and generated the .log file
(attached herewith) successfully.
The input file (.com file) which i used for this was:

%chk=mol41
#P LANL2MB opt freq
mol41, LANL2MB, 1/9-05
0 1
C -0.2056 1.2887 -1.0386
O -0.0738 0.2026 -0.1193
C -1.3831 -0.3364 0.0735
C -1.7263 -0.3218 1.5645
N -1.7431 1.0610 2.0481
C -1.9219 1.3140 3.3598
O -2.0693 0.3946 4.1417
C -1.9389 2.7065 3.8468
C -1.7757 3.7662 2.9511
C -1.7930 5.0645 3.4123
C -1.9715 5.3248 4.7613
C -2.1339 4.2871 5.6573
C -2.1245 2.9742 5.2098
O -2.2840 1.9536 6.0891
C -2.4366 2.5424 7.3821
C -2.6189 1.4559 8.4105
O -2.6182 0.2964 8.0709
O -2.7821 1.7764 9.7037
C -1.4237 -1.7753 -0.4450
Hg -1.1165 -1.7796 -2.5224
O -0.8313 -1.7837 -4.4515
H 0.7828 1.6721 -1.2920
H -0.7032 0.9404 -1.9436
H -0.7968 2.0821 -0.5813
H -2.1085 0.2670 -0.4722
H -2.7075 -0.7716 1.7159
H -0.9770 -0.8903 2.1153
H -1.6255 1.7945 1.4243
H -1.6359 3.5680 1.8987
H -1.6664 5.8829 2.7191
H -1.9833 6.3455 5.1141
H -2.2726 4.4980 6.7074
H -1.5477 3.1253 7.6232
H -3.3101 3.1943 7.3837
H -2.8991 1.0793 10.3635
H -0.6404 -2.3583 0.0393
H -2.3954 -2.2152 -0.2205
H -0.8643 -2.7070 -4.7370
--link1--
%chk=mol41
#p Geom=AllCheckpoint guess=read LANL2MB Pop=(MK,ReadRadii)
Hg 2.0
Here i used LANL2MB basis set as the molecule contains Hg (mercury). Also,
i used Pop=(MK,ReadRadii) to set the Hg radius in Gaussian.

Since i wanted to again convert this log file into mol2 so i ran
antechamber-

$ antechamber -i mol41.log -fi gout -o mol41.mol2 -fo mol2 -c resp

The error message came out as -

For atom[10]:Hg1, the best APS is not zero, exit
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 "/opt/n1ge6/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit

Also, ANTERCHAMBER.esp file could not be formed as RESP understands
HF/6-31g* pop=MK Iop(6/33=2) to get electrostatic points from Gaussian.
Could anyone help me out in solving this problem?

Thanks,
Megha


  • application/octet-stream attachment: mol41.rar

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