AMBER Archive (2009)

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

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Oct 29 2009 - 10:45:27 CDT

There are two problems.

First of all, no ESP were printed out in your Gaussian log file, therefore
it is not possible to get resp charges. You may use antechamber to generate
the input for Gaussian calculation. By default, input generated by
antechamber has proper keywords to generate ESP. Certainly, for your
molecule, you need to manually replace HF with LANL2MB

Secondly, you need to append one more line to the file
$AMBERHOME/dat/antechamber/APS.DAT to make bondtype function properly.
APS Hg 80 2 * * 0 * *
* * *

Then you can run the following antechamber command:
antechamber -fi gout -fo mol2 -i gaussian.log -o mol.mol2 -c resp

Best

Junmei

On Wed, Oct 28, 2009 at 3:00 AM, megha bajaj <micro.megha_at_gmail.com> wrote:

> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber