AMBER Archive (2003)

Subject: Re: AMBER: RESP charges

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Thu Dec 11 2003 - 10:41:45 CST

Hi Junmei,
 After the g98 log file was converted to ac file with antechamber "antechamber
-i g98.log -fi gout -o g98.ac -fo ac -nc -2", the all atoms don't have
charges in the ac file. Do you have any clue what is wrong?
Thanks.

Youyi

The ac file looks like this:
CHARGE 0.00
Formula: H19C6N2O14Mg1P3
ATOM 1 C1 MOL 1 -4.703 -2.167 -1.268 0.000000
C C
ATOM 2 H1 MOL 1 -5.178 -2.874 -0.588 0.000000
H H
ATOM 3 H2 MOL 1 -4.670 -1.168 -0.834 0.000000
H H
ATOM 4 H3 MOL 1 -5.200 -2.147 -2.238 0.000000
H H
ATOM 5 N1 MOL 1 -3.319 -2.611 -1.481 0.000000
N N
ATOM 6 H4 MOL 1 -2.843 -1.956 -2.118 0.000000
H H
ATOM 7 H5 MOL 1 -2.823 -2.634 -0.579 0.000000
H H
ATOM 8 H6 MOL 1 -3.320 -3.553 -1.896 0.000000
H H
ATOM 9 P1 MOL 1 0.581 2.471 -0.734 0.000000
P P
ATOM 10 O1 MOL 1 0.017 3.875 -0.609 0.000000
O O
.
.
.
.
BOND 1 1 2 1 C1 H1
BOND 2 1 3 1 C1 H2
BOND 3 1 4 1 C1 H3
BOND 4 1 5 1 C1 N1
BOND 5 5 6 1 N1 H4
BOND 6 5 7 1 N1 H5
BOND 7 5 8 1 N1 H6
BOND 8 9 10 2 P1 O1
BOND 9 9 11 9 P1 O2
.
.

Junmei Wang wrote:

> In this situation, prepgen can't work properly. You may solve this problem
> as the following: generate an ac file from gaussian output file; generate
> resp input file with respgen and do modifications (you want to the metal to
> bear an integer charge); run resp to get resp charges and read in to the ac
> file with antechamber; For each residue, extract the corresponding part
> from the ac file (you may ignore the bond connection information) to form a
> mpdb file; for each residue, read in the mpdb file and generate the prep
> input file with antechamber. This procedure should work for you.
>
> Best
>
> Junmei
>
> ===============================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals
> 7000 Fannin, Houston TX 77030
> Tel: 713-5786649
> Email: jwang_at_tbc.com
> Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
> ===============================================================
>
>
> Youyi Peng
> <pengyo_at_UMDNJ.EDU
> > To
> Sent by: amber_at_scripps.edu
> owner-amber_at_scrip cc
> ps.edu
> Subject
> Re: AMBER: RESP charges
> 12/10/2003 04:48
> PM
>
>
> Please respond to
> amber_at_scripps.edu
>
>
>
> IN the origonal mol2 file every atom has different name. But after mol2
> file
> was converted to g98 input gcrt file with antechamber, the same atom has
> the
> same name. And so does every atom in the g98 output log file. I need to
> point
> out here is that my system is not a single molecule but a hexacoordination
> system including four molecules and a metal ion. Does antechamber apply to
> this situation?
> Thanks.
>
> Youyi
>
> "David A. Case" wrote:
>
> > On Wed, Dec 10, 2003, Youyi Peng wrote:
> >
> > > resp.prepi file goes here:
> > >
> > > 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
> >
> > Are all of your atom names unique? Note that antechamber requires that
> > everything be in a single residue, and that no duplicate atom names
> appear.
> >
> > ..hope this helps...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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