AMBER Archive (2003)

Subject: Re: AMBER: RESP charges

From: Jiten (jiten_at_postech.ac.kr)
Date: Wed Dec 10 2003 - 11:55:51 CST

Hai Youyi Peng,

Check if the numbers just after ESP Fit Center and Just before Fit in the
Gaussian Output file. If the numbers are more than 9999 gaussian will print
****. You need to modify it.

Anyway iop(6/33=2) iop(6/41=10) iop(6/42=6) does not give better RESP
fitting. In my calculations I find iop(6/33=2) gives better charge fitting
than using many Iop options. If you are using only iop(6/33=2) , you will
not have this kind of problems becuase it generates less centers.

Hope this will help you.

Best wishes,

Jiten

----- Original Message -----
From: "Youyi Peng" <pengyo_at_UMDNJ.EDU>
To: <amber_at_scripps.edu>
Sent: Thursday, December 11, 2003 2:28 AM
Subject: Re: AMBER: RESP charges

> Yes. The g98 job complete successfully. I found these word at the end of
the
> g98.log file " Normal termination of Gaussian 98." The input for g98 is
as
> followed and the input coordinate file was generated with antechamber
> "antechamber -i x.mol2 -fi mol2 -o g98.gcart -fo gcart".
>
> gp8.inp goes here
> "%chk=gausesp.chk
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/41=10) iop(6/42=6)
>
> remark line goes here
>
> -2 1
> 45 atoms' coordinates."
>
> THen I used the command line: " antechamber -i g98.log -fi gout -o
resp.prepi
> -fo prepi -c resp -s 2 -nc 2 " to calculate RESP charges. The resp.prepi
file is
> as followed. The residue fragments don't have charges and angle values.
ANd the
> torsion values are also strange.
>
> resp.prepi file goes here:
>
> 0 0 2
>
> This is a remark line
> molecule.res
> MOL XYZ 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 O1 o M 3 2 1 1.540 111.208 180.000 -0.874
> 5 P1 p5 M 4 3 2 1.518 111.808 5.088 1.242
> 6 O2 o E 5 4 3 1.515 117.779 -169.220 -0.874
> 7 O3 o E 5 4 3 1.568 100.818 76.435 -0.874
> 8 O6 os M 5 4 3 1.604 109.962 -36.819 -0.504
> 9 P2 p5 M 8 5 4 1.605 119.079 62.039 1.296
> 10 O4 o E 9 8 5 1.486 102.591 -85.747 -0.808
> 11 O5 o E 9 8 5 1.425 117.678 39.649 -0.808
> 12 O9 os M 9 8 5 1.595 102.944 159.262 -0.547
> 13 P3 p5 M 12 9 8 1.562 130.640 9.668 1.368
> 14 O7 o E 13 12 9 1.465 112.843 -144.746 -0.838
> 15 O8 o E 13 12 9 1.528 116.248 -21.300 -0.838
> 16 O10 os M 13 12 9 1.592 106.308 87.685 -0.529
> 17 C2 c3 M 16 13 12 1.427 136.700 -55.054 0.153
> 18 H7 h1 E 17 16 13 1.090 108.895 -137.317 0.035
> 19 H8 h1 E 17 16 13 1.089 108.946 102.607 0.035
> 20 H9 h1 E 17 16 13 1.090 108.869 -17.363 0.035
> 21 X 1 0 1 4.337 nan 496.982 0.000
> 22 X 1 0 1 4.337 nan 496.982 0.000
> 23 X 1 0 1 4.337 nan 496.982 0.000
> 24 X 1 0 1 4.337 nan 496.982 0.000
> 25 X 1 0 1 4.337 nan 496.982 0.000
> 26 X 1 0 1 4.337 nan 496.982 0.000
> 27 X 1 0 1 4.337 nan 496.982 0.000
> 28 X 1 0 1 4.337 nan 496.982 0.000
> 29 X 1 0 1 4.337 nan 496.982 0.000
> 30 X 1 0 1 4.337 nan 496.982 0.000
> 31 X 1 0 1 4.337 nan 496.982 0.000
> 32 X 1 0 1 4.337 nan 496.982 0.000
> 33 X 1 0 1 4.337 nan 496.982 0.000
> 34 X 1 0 1 4.337 nan 496.982 0.000
> 35 X 1 0 1 4.337 nan 496.982 0.000
> 36 X 1 0 1 4.337 nan 496.982 0.000
> 37 X 1 0 1 4.337 nan 496.982 0.000
> 38 X 1 0 1 4.337 nan 496.982 0.000
> 39 X 1 0 1 4.337 nan 496.982 0.000
> 40 X 1 0 1 4.337 nan 496.982 0.000
> 41 X 1 0 1 4.337 nan 496.982 0.000
> 42 X 1 0 1 4.337 nan 496.982 0.000
> 43 X 1 0 1 4.337 nan 496.982 0.000
> 44 X 1 0 1 4.337 nan 496.982 0.000
> 45 X 1 0 1 4.337 nan 496.982 0.000
> 46 X 1 0 1 4.337 nan 496.982 0.000
> 47 X 1 0 1 4.337 nan 496.982 0.000
>
> Thanks a lot in advance.
>
> Youyi
>
>
> > On Wed, Dec 10, 2003, Youyi Peng wrote:
> >
> > > I am trying to calculate RESP charges for a coordination system which
> > > consists of a metal ion and several residue fragments. I used
antechamber in
> > > AMBER7.0 to perform this job. After the esp charge calculation with
> > > Gaussian98, I typed the command: antechamber -i g98.log -fi gout -o
> > > resp.prepi -fo prepi -c resp -s 2 -nc 2. Then I checked the resp
charges in
> > > th efile resp.prepi and found the charges for the residue fragments
are all
> > > zero. I guess this easy way to calculate RESP charges doesn't work for
the
> > > fragments. What should I do? Do I need to go the traditional way?
> > > Any suggestions are highly appreciated.
> > >
> >
> > Did the Gaussian job complete successfully (check the g98.log file)? If
so,
> > we would need more detailed information to be of much help.
> >
> > ..regards...dac
> >
> > --
> >
> > ==================================================================
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> > ==================================================================
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