Thanks, Jiten:
The numbers after ESP Fit Center are printed ****. So you mean I need to modify
every line? My god, a lot of work.
Youyi
Jiten wrote:
> 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.UMDNJ.EDU>
> To: <amber.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.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
> > > ==================================================================
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 14 2004 - 15:53:07 PST
