AMBER Archive (2008)

Subject: Re: AMBER: Generating RESP charges

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Feb 19 2008 - 13:22:59 CST

Hi, Christ,
I took a look at your gaussian output file. It does not contain the
identifier of "Standard orientation:" after the line that has the identifier
of "Optimization completed.". Therefore no coordinates are read in by
antechamber at all. If you use the gaussian input files generated by
antechamber, that identifier is always there. Anyway, I will fix the code to
handle this kinds of special cases.

Now you may simply fix this problem yourself by changing the first "Input
orientation:" after the line of " Optimization completed." to "Standard
orientation:" in the gaussin output file. That is to say:
change line 14892 to " Standard orientation:"

Best

Junmei

On Feb 19, 2008 12:38 PM, M. L. Dodson <activesitedynamics_at_comcast.net>
wrote:

> Junmei Wang wrote:
> > Hi, Chris
> > I just prepared a pdb file and used it as the input. The pdb file was
> > generated based the date in your last email. Therefore the files I send
> > to you contained no charges. If you send me the gaussian output file, I
> > would like to generate prep input file for you. The net charge
> > information is read from the gaussian output file.
> >
> > Best
> >
> > Junmei
> >
>
> I looked at the pdb file in a viewer, and it mostly looked like a
> bunch of separated atoms, not a structure that pymol could interpret.
> I suspect the input structure is the basic problem.
>
> Bud Dodson
>
> > On Feb 19, 2008 10:11 AM, Christopher Illingworth
> > <christopher.illingworth_at_chem.ox.ac.uk
> > <mailto:christopher.illingworth_at_chem.ox.ac.uk>> wrote:
> >
> > Hi Junmei,
> >
> > I am using amber9. I might be getting confused, but does the
> prepin
> > file
> > you sent contain charges? I can get something like it by
> converting pdb
> > to mol2 to prepin, but I would like to use my Gaussian output to
> get
> > RESP
> > charges, which I think are contained in the right-most column of
> the
> > .prepin file (AM1 charges work fine for me).
> >
> > If in Gaussian I use a non-correct zero charge on the ligand and
> use the
> > output as an input to antechamber I end up with this .prepin file:
> >
> > 0 0 2
> >
> > This is a remark line
> > molecule.res
> > MOL INT 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
> 1.44165
> > 5 C1 c M 4 3 2 1.236 75.380 0.527 -
> 2.20230
> > 6 O2 o E 5 4 3 1.226 129.621 0.560
> 1.44165
> > 7 C2 c M 5 4 3 1.577 114.792 -179.551 -
> 3.44216
> > 8 O3 o E 7 5 4 1.215 122.892 179.171
> 0.90370
> > 9 N1 n M 7 5 4 1.340 114.555 -0.816
> 7.15808
> > 10 H3 hn E 9 7 5 0.996 118.619 0.317 -
> 2.92119
> > 11 C3 c3 M 9 7 5 1.441 123.613 179.853 -
> 7.58477
> > 12 H1 h1 E 11 9 7 1.088 110.525 58.393
> 1.98070
> > 13 H2 h1 E 11 9 7 1.087 110.617 -58.115
> 1.98070
> > 14 C4 c M 11 9 7 1.550 113.882 -179.921 -
> 1.90124
> > 15 O5 o E 14 11 9 1.233 117.414 0.264
> 1.57259
> > 16 O4 o M 14 11 9 1.239 113.680 -179.825
> 1.57259
> >
> >
> > LOOP
> >
> > IMPROPER
> > C2 O1 C1 O2
> > C1 N1 C2 O3
> > C3 O5 C4 O4
> >
> > DONE
> > STOP
> >
> > I think that the last column of numbers, which are zero in your
> > file, are
> > the charges, which in this case are not correct.
> >
> > When I run Gaussian with a correct -2 charge on the ligand, I only
> get
> > this:
> >
> > 0 0 2
> >
> > This is a remark line
> > molecule.res
> > MOL INT 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
> >
> >
> > LOOP
> >
> > IMPROPER
> >
> > DONE
> > STOP
> >
> > Am I expecting numbers where I shouldn't actually be getting them?
> >
> > Thanks,
> >
> > Chris
> >
> >
> >
> > On Tue, 19 Feb 2008, Junmei Wang wrote:
> >
> > > Hi, Chris,
> > > Which version of amber or antechamber do you use? I tested this
> > molecule
> > > using both amber9 and amber10, both work fine. Here is the input
> > and output
> > > files.
> > >
> > > Best
> > >
> > > Junmei
> > >
> >
> -------------------------------------------------------------------------
> > > input in pdb
> > >
> >
> -------------------------------------------------------------------------
> > > ATOM 1 C1 MOL 1 0.9424 -0.0505 -2.4332
> > > ATOM 2 C2 MOL 1 1.1055 -0.0641 -0.8649
> > > ATOM 3 C3 MOL 1 -0.1251 0.0046 1.2536
> > > ATOM 4 C4 MOL 1 -1.5720 0.0899 1.8035
> > > ATOM 5 O1 MOL 1 -0.2256 0.0053 -2.8330
> > > ATOM 6 O2 MOL 1 1.9873 -0.0961 -3.0745
> > > ATOM 7 O3 MOL 1 2.1868 -0.1312 -0.3151
> > > ATOM 8 O4 MOL 1 -1.6348 0.0922 3.0406
> > > ATOM 9 N1 MOL 1 -0.0468 0.0051 -0.1853
> > > ATOM 10 O5 MOL 1 -2.4892 0.1446 0.9805
> > > ATOM 11 H1 MOL 1 0.4404 0.8364 1.6668
> > > ATOM 12 H2 MOL 1 0.3359 -0.8925 1.6606
> > > ATOM 13 H3 MOL 1 -0.8999 0.0532 -0.6966
> > >
> > >
> >
> ----------------------------------------------------------------------------
> > > output in mol2 and prepi
> > >
> >
> ----------------------------------------------------------------------------
> > > @<TRIPOS>MOLECULE
> > > MOL
> > > 13 12 1 0 0
> > > SMALL
> > > No Charge or Current Charge
> > >
> > >
> > > @<TRIPOS>ATOM
> > > 1 C1 0.9420 -0.0510 -2.4330 C.2 1 MOL
> > 0.000000
> > > 2 C2 1.1050 -0.0640 -0.8650 C.2 1 MOL
> > 0.000000
> > > 3 C3 -0.1250 0.0050 1.2540 C.3 1 MOL
> > 0.000000
> > > 4 C4 -1.5720 0.0900 1.8040 C.2 1 MOL
> > 0.000000
> > > 5 O1 -0.2260 0.0050 -2.8330 O.co2 1 MOL
> > 0.000000
> > > 6 O2 1.9870 -0.0960 -3.0750 O.co2 1 MOL
> > 0.000000
> > > 7 O3 2.1870 -0.1310 -0.3150 O.2 1 MOL
> > 0.000000
> > > 8 O4 -1.6350 0.0920 3.0410 O.co2 1 MOL
> > 0.000000
> > > 9 N1 -0.0470 0.0050 -0.1850 N.am <http://N.am>
> > 1 MOL 0.000000
> > > 10 O5 -2.4890 0.1450 0.9810 O.co2 1 MOL
> > 0.000000
> > > 11 H1 0.4400 0.8360 1.6670 H 1 MOL
> > 0.000000
> > > 12 H2 0.3360 -0.8920 1.6610 H 1 MOL
> > 0.000000
> > > 13 H3 -0.9000 0.0530 -0.6970 H 1 MOL
> > 0.000000
> > > @<TRIPOS>BOND
> > > 1 1 2 1
> > > 2 1 5 1
> > > 3 1 6 1
> > > 4 2 7 2
> > > 5 2 9 am
> > > 6 3 4 1
> > > 7 3 9 1
> > > 8 3 11 1
> > > 9 3 12 1
> > > 10 4 8 1
> > > 11 4 10 1
> > > 12 9 13 1 0 0 2
> > >
> > > This is a remark line
> > > molecule.res
> > > MOL INT 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
> > 0.000000
> > > 5 C1 c M 4 3 2 1.236 160.924 -82.030
> > 0.000000
> > > 6 O2 o E 5 4 3 1.227 129.574 171.882
> > 0.000000
> > > 7 C2 c M 5 4 3 1.577 114.835 -8.219
> > 0.000000
> > > 8 O3 o E 7 5 4 1.216 122.853 179.187
> > 0.000000
> > > 9 N1 n M 7 5 4 1.340 114.555 -0.820
> > 0.000000
> > > 10 H3 hn E 9 7 5 0.996 118.558 0.331
> > 0.000000
> > > 11 C3 c3 M 9 7 5 1.441 123.604 179.906
> > 0.000000
> > > 12 H1 h1 E 11 9 7 1.086 110.575 58.331
> > 0.000000
> > > 13 H2 h1 E 11 9 7 1.088 110.533 -58.185
> > 0.000000
> > > 14 C4 c M 11 9 7 1.550 113.876 -179.892
> > 0.000000
> > > 15 O5 o E 14 11 9 1.233 117.364 0.140
> > 0.000000
> > > 16 O4 o M 14 11 9 1.239 113.695 -179.887
> > 0.000000
> > >
> > >
> > > LOOP
> > >
> > > IMPROPER
> > > C2 O1 C1 O2
> > > C1 N1 C2 O3
> > > C3 O5 C4 O4
> > >
> > > DONE
> > > STOP
> > >
> > > @<TRIPOS>SUBSTRUCTURE
> > > 1 MOL 1 TEMP 0 **** **** 0 ROOT
> > >
> > >
> > >
> > > On Feb 19, 2008 5:39 AM, Christopher Illingworth <
> > > christopher.illingworth_at_chem.ox.ac.uk
> > <mailto:christopher.illingworth_at_chem.ox.ac.uk>> wrote:
> > >
> > >> I am having difficulty generating RESP charges for a ligand -
> > does anyone
> > >> know what I am doing wrong? I have proceeded as follows:
> > >>
> > >> 1. Optimise the ligand geometry using Gaussian03. My input
> > line is as
> > >> follows:
> > >>
> > >> #p opt hf/6-31G* Geom=Checkpoint NoSymm Pop=MK
> IOp(6/33=2,6/42=6)
> > >>
> > >> This gives a list of about 5000 ESP fit centres, and I can
> > generate a .esp
> > >> file which looks fine.
> > >>
> > >> 2. Run antechamber as follows:
> > >>
> > >> antechamber -i file.log -fi gout -o file.prepin -fo prepi -c
> > resp -nc -2
> > >>
> > >> I don't get any error messages from this, but my .prepin file
> > does not
> > >> contain any of the atoms, just dummy atoms. There seems to be
> a
> > problem
> > >> with the .ac file ANTECHAMBER_AC.AC, which contains only this:
> > >>
> > >> CHARGE -2.00 ( 0 )
> > >> Formula:
> > >>
> > >> If in the first place when I run Gaussian on the ligand I
> > pretend it has
> > >> zero charge (for example if I use antechamber to generate a
> > Gaussian input
> > >> file and submit that), I do get a .prepin file, but the charges
> > are all
> > >> wrong (i.e. magnitude up to 7.5).
> > >>
> > >> Am I doing something wrong, or is there a problem in
> antechamber
> > with
> > >> charged ligands?
> > >>
> > >> My ligand coordinates are as follows:
> > >>
> > >> C 0.9424 -0.0505 -2.4332
> > >> C 1.1055 -0.0641 -0.8649
> > >> C -0.1251 0.0046 1.2536
> > >> C -1.5720 0.0899 1.8035
> > >> O -0.2256 0.0053 -2.8330
> > >> O 1.9873 -0.0961 -3.0745
> > >> O 2.1868 -0.1312 -0.3151
> > >> O -1.6348 0.0922 3.0406
> > >> N -0.0468 0.0051 -0.1853
> > >> O -2.4892 0.1446 0.9805
> > >> H 0.4404 0.8364 1.6668
> > >> H 0.3359 -0.8925 1.6606
> > >> H -0.8999 0.0532 -0.6966
> > >>
> > >> Thanks,
> > >>
> > >> Chris
> > >>
> > >>
> > >>
> >
> -----------------------------------------------------------------------
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> >
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>
>
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
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