AMBER Archive (2008)

Subject: Re: AMBER: Generating RESP charges

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Feb 19 2008 - 12:04:44 CST

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

On Feb 19, 2008 10:11 AM, Christopher Illingworth <
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 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> 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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