AMBER Archive (2008)

Subject: Re: AMBER: Generating RESP charges

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Feb 19 2008 - 09:05:39 CST

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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