AMBER Archive (2003)

Subject: Re: AMBER: Antechamber formal charges with Gasteiger method

From: Junmei Wang (JWang_at_encysive.com)
Date: Tue Aug 26 2003 - 14:55:14 CDT

It is a good suggestion for us to judge net charges of molecues with
atomtype. I will check what tripos people did and design the defination
file for atomtype.

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
===============================================================

                                                                           
             "Lee, Matthew"
             <mrlee_at_amgen.com>
             Sent by: To
             owner-amber_at_scrip "'amber_at_scripps.edu'"
             ps.edu <amber_at_scripps.edu>
                                                                        cc
                                                                           
             08/26/2003 01:07 Subject
             PM AMBER: Antechamber formal charges
                                       with Gasteiger method
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           
                                                                           

Hello--

 In antechamber, the -c gas Gasteiger charge method does not seem to
work correctly with the -nc arg set to a formal charge on molecules that
have correct explicit protonation states. The charges produced still sum
up
to 0. (And btw, I did apply bugfix.17, which is not related to this
problem.)

 Ultimately, it would be nice if antechamber's chemical perception
engine could recognize that these oxygens are part of an acid and thus give
this functional group a contribution of -1 to the total formal charge of
the
molecule. When Sybyl assigns Gasteiger charges on this same acid.mol2
file,
it does just that, correctly identifying this molecule has having a formal
charge of -1, and assigning atomic charges that sum up to -1. I am unable
to get antechamber to do just the latter part, after explicitly specifying
a
formal charge of -1 with "-nc -1".

 Below is a simple carboxylate acid.mol2 input file on which I used
the following command and the output:

antechamber -i acid.mol2 -fi mol2 -o acid_gstgr.mol2 -fo mol2 -nc -1 -c gas
--------------------------------------------------
@<TRIPOS>MOLECULE
test_acid
   13 12 1 0 0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1 C1 24.6493 8.1810 33.0721 C.3 1 <1>
0.0000
      2 H1 24.3127 8.1636 32.0250 H 1 <1>
0.0000
      3 H2 23.8707 8.6387 33.7000 H 1 <1>
0.0000
      4 H3 24.8383 7.1527 33.4138 H 1 <1>
0.0000
      5 H4 26.3486 8.6326 31.0822 H 1 <1>
0.0000
      6 H5 27.2324 9.9983 31.8441 H 1 <1>
0.0000
      7 H6 25.4963 10.1775 31.4194 H 1 <1>
0.0000
      8 O2 24.8248 10.0283 35.0474 O.co2 1 <1>
0.0000
      9 C18 25.6482 10.1245 34.1051 C.2 1 <1>
0.0000
     10 O3 26.2869 11.1915 33.9364 O.co2 1 <1>
0.0000
     11 C19 25.8703 8.9564 33.1744 C.3 1 <1>
0.0000
     12 C20 26.2651 9.4785 31.7804 C.3 1 <1>
0.0000
     13 H20 26.6675 8.3277 33.5654 H 1 <1>
0.0000
@<TRIPOS>BOND
     1 1 2 1
     2 1 3 1
     3 11 1 1
     4 1 4 1
     5 12 5 1
     6 12 6 1
     7 12 7 1
     8 8 9 ar
     9 9 10 ar
    10 9 11 1
    11 11 12 1
    12 11 13 1
@<TRIPOS>SUBSTRUCTURE
     1 **** 8 TEMP 0 **** **** 0 ROOT
--------------------------------------------------
Here are the atom records from the acid_gstgr.mol2 outupt file:
@<TRIPOS>ATOM
      1 C1 24.6490 8.1810 33.0720 c3 1 <1>
-0.0521
      2 H1 24.3130 8.1640 32.0250 hc 1 <1>
0.0239
      3 H2 23.8710 8.6390 33.7000 hc 1 <1>
0.0239
      4 H3 24.8380 7.1530 33.4140 hc 1 <1>
0.0239
      5 H4 26.3490 8.6330 31.0820 hc 1 <1>
0.0239
      6 H5 27.2320 9.9980 31.8440 hc 1 <1>
0.0239
      7 H6 25.4960 10.1780 31.4190 hc 1 <1>
0.0239
      8 O2 24.8250 10.0280 35.0470 o 1 <1>
-0.2470
      9 C18 25.6480 10.1240 34.1050 c 1 <1>
0.3577
     10 O3 26.2870 11.1910 33.9360 o 1 <1>
-0.2470
     11 C19 25.8700 8.9560 33.1740 c3 1 <1>
0.0557
     12 C20 26.2650 9.4790 31.7800 c3 1 <1>
-0.0521
     13 H20 26.6680 8.3280 33.5650 hc 1 <1>
0.0416

--Matthew Lee

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