AMBER Archive (2003)

Subject: Re: AMBER: RESP charges

From: Junmei Wang (JWang_at_encysive.com)
Date: Thu Dec 18 2003 - 15:17:28 CST

It seems that the charges you listed is from the first stage. Are you sure
you generated the charges for the second stage properly? Please send me the
output files of resp so I can help you to figure out what is the problem.
To my opinion, the charges are pretty reasonable. Typically, phosphates do
bear pretty large charges.

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
             12/18/2003 09:20
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

Hi Junmei,
Following your instructions, I went through all the procedure to calculate
RESP charges. However, the resp charges from the first and second stage
fitting didn't change at all and have very high value. Something must be
wrong.
My system includes six single molecules (a Mg coordination system). But all
g98, antechamber and resp treat it as one single molecule. All tutorial and
information seem suitable for only single molecule. I don't know what to
deal
with the situation. I list my mol2, gcrt,ac and respin files here, and also
the resp chareges I got for this system. Would you please take a while to
look
at how to modify these files.
Thanks a lot.

Youyi Peng

mol2 file
@<TRIPOS>MOLECULE
MGSYS
   45 39 6 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
      1 CE 38.0430 60.6410 7.1880 C.3 1 LYS+33
-0.1030
****
      2 HE3 38.1579 61.6791 6.8761 H 1 LYS+33
0.0660
****
      3 HE1 37.2002 60.1703 6.6818 H 1 LYS+33
0.0660
****
      4 HE2 37.9358 60.5554 8.2693 H 1 LYS+33
0.0660
****
      5 NZ 39.2610 59.9180 6.7990 N.3 1 LYS+33
-0.0730
****
      6 HZ1 39.1779 58.9298 7.0773 H 1 LYS+33
0.3260
****
      7 HZ2 39.3849 59.9775 5.7782 H 1 LYS+33
0.3260
****
      8 HZ3 40.0755 60.3390 7.2684 H 1 LYS+33
0.3260
****
      9 PG 37.5270 54.4619 3.8299 P 2 ATP381
1.4930
****
     10 O1G 36.0790 54.0039 3.8239 O.2 2 ATP381
-0.9130
****
     11 O2G 38.5130 53.6969 2.9709 O.2 2 ATP381
-0.9130
****
     12 O3G 37.9270 54.1519 5.3139 O.2 2 ATP381
-0.9130
****
     13 PB 36.9230 57.0059 4.7339 P 2 ATP381
1.3340
****
     14 O1B 35.5110 57.0769 4.2769 O.2 2 ATP381
-0.9130
****
     15 O2B 37.0600 56.6369 6.1029 O.2 2 ATP381
-0.9130
****
     16 O3B 37.5990 56.0519 3.6339 O.3 2 ATP381
-0.5080
****
     17 PA 38.6220 58.8639 3.3589 P 2 ATP381
1.3340
****
     18 O1A 39.6740 59.7669 3.8329 O.2 2 ATP381
-0.9130
****
     19 O2A 39.3220 57.7569 2.5729 O.2 2 ATP381
-0.9130
****
     20 O3A 37.6620 58.3999 4.4999 O.3 2 ATP381
-0.5080
****
     21 O5* 37.6940 59.4409 2.2009 O.3 2 ATP381
-0.4910
****
     22 C5* 36.5940 58.9739 1.4229 C.3 2 ATP381
0.0390
****
     23 H5*3 36.7413 59.2754 0.3858 H 2 ATP381
0.0660
****
     24 H5*1 35.6748 59.4119 1.8117 H 2 ATP381
0.0660
****
     25 H5*2 36.5479 57.8871 1.4924 H 2 ATP381
0.0660
****
     26 MG 39.5010 55.7059 2.7639 Mg 3 MG383
2.0000
****
     27 CB 43.3161 55.2559 0.8887 C.3 4 ASN132
-0.2930
****
     28 HB3 42.9768 55.9158 0.0903 H 4 ASN132
0.0660
****
     29 HB1 43.9554 55.7978 1.5857 H 4 ASN132
0.0660
****
     30 HB2 43.8686 54.3951 0.5121 H 4 ASN132
0.0660
****
     31 CG 42.0841 54.7459 1.6547 C.2 4 ASN132
0.7260
****
     32 OD1 41.0571 55.4209 1.5367 O.2 4 ASN132
-0.4920
****
     33 ND2 42.1431 53.6889 2.5147 N.3 4 ASN132
-0.6870
****
     34 HD21 43.0105 53.1396 2.5969 H 4 ASN132
0.2740
****
     35 HD22 41.3202 53.4400 3.0820 H 4 ASN132
0.2740
****
     36 O 38.2370 55.5959 1.0426 O.3 5 HOH111
-0.8200
****
     37 HO1 39.2670 55.5959 1.0426 H 5 HOH111
0.4100
****
     38 HO2 37.8932 56.5668 1.0426 H 5 HOH111
0.4100
****
     39 CB 42.1651 57.1282 3.9506 C.3 6 ASP-145
-0.2930
****
     40 HB3 42.7444 57.8504 4.5259 H 6 ASP-145
0.0660
****
     41 HB1 42.8388 56.4040 3.4926 H 6 ASP-145
0.0660
****
     42 HB2 41.6064 57.6476 3.1720 H 6 ASP-145
0.0660
****
     43 CG 41.2021 56.4102 4.8676 C.2 6 ASP-145
0.6790
****
     44 OD1 41.2281 56.6912 6.0816 O.2 6 ASP-145
-0.7920
****
     45 OD2 40.4021 55.5492 4.4356 O.2 6 ASP-145
-0.7920
****
@<TRIPOS>BOND
    1 1 5 1
    2 1 3 1
    3 1 4 1
    4 1 2 1
    5 5 6 1
    6 5 7 1
    7 5 8 1
    8 9 10 1
    9 9 11 1
   10 9 12 1
   11 9 16 1
   12 13 14 1
   13 13 15 1
   14 13 16 1
   15 13 20 1
   16 17 18 1
   17 17 19 1
   18 17 20 1
   19 17 21 1
   20 21 22 1
   21 22 24 1
   22 22 25 1
   23 22 23 1
   24 27 31 1
   25 27 29 1
   26 27 30 1
   27 27 28 1
   28 31 32 2
   29 31 33 ar
   30 33 34 1
   31 33 35 1
   32 36 37 1
   33 36 38 1
   34 39 43 1
   35 39 41 1
   36 39 42 1
   37 39 40 1
   38 43 44 ar
   39 43 45 ar
@<TRIPOS>SUBSTRUCTURE
      1 LYS+33 1 RESIDUE 0 A LYS+
      2 ATP381 9 **** 0 A ATP
      3 MG383 26 **** 0 A MG
      4 ASN132 27 RESIDUE 0 A ASN
      5 HOH111 36 **** 0 Z HOH
      6 ASP-145 39 RESIDUE 0 A ASP-

gcrt file
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

remark line goes here

-2 1
    C 38.0430 60.6410 7.1880
    H 38.1579 61.6791 6.8761
    H 37.2002 60.1703 6.6818
    H 37.9358 60.5554 8.2693
    N 39.2610 59.9180 6.7990
    H 39.1779 58.9298 7.0773
    H 39.3849 59.9775 5.7782
    H 40.0755 60.3390 7.2684
    P 37.5270 54.4619 3.8299
    O 36.0790 54.0039 3.8239
    O 38.5130 53.6969 2.9709
    O 37.9270 54.1519 5.3139
    P 36.9230 57.0059 4.7339
    O 35.5110 57.0769 4.2769
    O 37.0600 56.6369 6.1029
    O 37.5990 56.0519 3.6339
    P 38.6220 58.8639 3.3589
    O 39.6740 59.7669 3.8329
    O 39.3220 57.7569 2.5729
    O 37.6620 58.3999 4.4999
    O 37.6940 59.4409 2.2009
    C 36.5940 58.9739 1.4229
    H 36.7413 59.2754 0.3858
    H 35.6748 59.4119 1.8117
    H 36.5479 57.8871 1.4924
   Mg 39.5010 55.7059 2.7639
    C 43.3161 55.2559 0.8887
    H 42.9768 55.9158 0.0903
    H 43.9554 55.7978 1.5857
    H 43.8686 54.3951 0.5121
    C 42.0841 54.7459 1.6547
    O 41.0571 55.4209 1.5367
    N 42.1431 53.6889 2.5147
    H 43.0105 53.1396 2.5969
    H 41.3202 53.4400 3.0820
    O 38.2370 55.5959 1.0426
    H 39.2670 55.5959 1.0426
    H 37.8932 56.5668 1.0426
    C 42.1651 57.1282 3.9506
    H 42.7444 57.8504 4.5259
    H 42.8388 56.4040 3.4926
    H 41.6064 57.6476 3.1720
    C 41.2021 56.4102 4.8676
    O 41.2281 56.6912 6.0816
    O 40.4021 55.5492 4.4356

ac file
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
ATOM 11 O2 MOL 1 2.066 2.283 -0.499 0.000000
O O
ATOM 12 O3 MOL 1 0.355 2.198 -2.261 0.000000
O O
ATOM 13 P2 MOL 1 -1.868 1.242 -0.356 0.000000
P P
ATOM 14 O4 MOL 1 -2.557 2.335 0.379 0.000000
O O
ATOM 15 O5 MOL 1 -2.161 1.221 -1.750 0.000000
O O
ATOM 16 O6 MOL 1 -0.336 1.438 0.081 0.000000
O O
ATOM 17 P3 MOL 1 -1.453 -1.087 1.267 0.000000
P P
ATOM 18 O7 MOL 1 -1.631 -2.516 0.996 0.000000
O O
ATOM 19 O8 MOL 1 0.053 -0.847 1.357 0.000000
O O
ATOM 20 O9 MOL 1 -2.239 -0.178 0.269 0.000000
O O
ATOM 21 O10 MOL 1 -1.868 -0.610 2.728 0.000000
O O
ATOM 22 C2 MOL 1 -1.869 0.615 3.459 0.000000
C C
ATOM 23 H7 MOL 1 -1.510 0.423 4.470 0.000000
H H
ATOM 24 H8 MOL 1 -2.885 1.007 3.491 0.000000
H H
ATOM 25 H9 MOL 1 -1.211 1.325 2.958 0.000000
H H
ATOM 26 Mg1 MOL 1 1.427 0.282 0.303 0.000000
Mg Mg
ATOM 27 C3 MOL 1 4.862 -2.175 0.966 0.000000
C C
ATOM 28 H10 MOL 1 4.584 -2.242 2.018 0.000000
H H
ATOM 29 H11 MOL 1 4.573 -3.083 0.436 0.000000
H H
ATOM 30 H12 MOL 1 5.932 -2.020 0.827 0.000000
H H
ATOM 31 C4 MOL 1 4.113 -0.987 0.339 0.000000
C C
ATOM 32 O11 MOL 1 3.104 -0.607 0.941 0.000000
O O
ATOM 33 N2 MOL 1 4.457 -0.461 -0.871 0.000000
N N
ATOM 34 H13 MOL 1 5.303 -0.794 -1.355 0.000000
H H
ATOM 35 H14 MOL 1 3.871 0.269 -1.301 0.000000
H H
ATOM 36 O12 MOL 1 1.519 1.510 2.052 0.000000
O O
ATOM 37 H15 MOL 1 2.137 0.716 1.832 0.000000
H H
ATOM 38 H16 MOL 1 0.672 1.166 2.525 0.000000
H H
ATOM 39 C5 MOL 1 1.552 -2.792 -0.728 0.000000
C C
ATOM 40 H17 MOL 1 1.163 -3.754 -1.063 0.000000
H H
ATOM 41 H18 MOL 1 2.641 -2.807 -0.765 0.000000
H H
ATOM 42 H19 MOL 1 1.226 -2.604 0.295 0.000000
H H
ATOM 43 C6 MOL 1 1.033 -1.697 -1.631 0.000000
C C
ATOM 44 O13 MOL 1 0.315 -2.024 -2.596 0.000000
O O
ATOM 45 O14 MOL 1 1.316 -0.493 -1.434 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
BOND 10 9 12 9 P1 O3
BOND 11 9 16 1 P1 O6
BOND 12 13 14 2 P2 O4
BOND 13 13 15 9 P2 O5
BOND 14 13 16 1 P2 O6
BOND 15 13 20 1 P2 O9
BOND 16 17 18 2 P3 O7
BOND 17 17 19 9 P3 O8
BOND 18 17 20 1 P3 O9
BOND 19 17 21 1 P3 O10
BOND 20 21 22 1 O10 C2
BOND 21 22 23 1 C2 H7
BOND 22 22 24 1 C2 H8
BOND 23 22 25 1 C2 H9
BOND 24 27 28 1 C3 H10
BOND 25 27 29 1 C3 H11
BOND 26 27 30 1 C3 H12
BOND 27 27 31 1 C3 C4
BOND 28 31 32 2 C4 O11
BOND 29 31 33 1 C4 N2
BOND 30 33 34 1 N2 H13
BOND 31 33 35 1 N2 H14
BOND 32 36 37 1 O12 H15
BOND 33 36 38 1 O12 H16
BOND 34 39 40 1 C5 H17
BOND 35 39 41 1 C5 H18
BOND 36 39 42 1 C5 H19
BOND 37 39 43 1 C5 C6
BOND 38 43 44 9 C6 O13
BOND 39 43 45 9 C6 O14

respin1
Resp charges for organic molecule

 &cntrl

 nmol = 1,
 ihfree = 1,
 ioutopt = 1,

 &end
    1.0
Resp charges for organic molecule
   -2 45
    6 0
    1 0
    1 0
    1 0
    7 0
    1 0
    1 6
    1 6
   15 0
    8 0
    8 10
    8 10
   15 0
    8 0
    8 14
    8 0
   15 0
    8 0
    8 18
    8 0
    8 0
    6 0
    1 0
    1 0
    1 0
   12 0
    6 0
    1 0
    1 0
    1 0
    6 0
    8 0
    7 0
    1 0
    1 34
    8 0
    1 0
    1 37
    6 0
    1 0
    1 0
    1 0
    6 0
    8 0
    8 44

respin2
Resp charges for organic molecule

 &cntrl

 nmol = 1,
 ihfree = 1,
 ioutopt = 1,
 iqopt = 2,
 qwt = 0.001,

 &end
    1.0
Resp charges for organic molecule
   -2 45
    6 0
    1 0
    1 2
    1 2
    7 -99
    1 -99
    1 -99
    1 -99
   15 -99
    8 -99
    8 -99
    8 -99
   15 -99
    8 -99
    8 -99
    8 -99
   15 -99
    8 -99
    8 -99
    8 -99
    8 -99
    6 0
    1 0
    1 23
    1 23
   12 -99
    6 0
    1 0
    1 28
    1 28
    6 -99
    8 -99
    7 -99
    1 -99
    1 -99
    8 -99
    1 -99
    1 -99
    6 0
    1 0
    1 40
    1 40
    6 -99
    8 -99
    8 -99

Resp charges for organic molecule

          Point Charges Before & After Optimization

    no. At.no. q(init) q(opt) ivary d(rstr)/dq
    1 6 0.000000 -0.002792 0 0.004998
    2 1 0.000000 0.031850 0 0.000000
    3 1 0.000000 0.115049 0 0.000000
    4 1 0.000000 0.055049 0 0.000000
    5 7 0.000000 -0.210419 0 0.002146
     6 1 0.000000 0.295469 0 0.000000
    7 1 0.000000 0.295469 6 0.000000
    8 1 0.000000 0.295469 6 0.000000
    9 15 0.000000 1.242491 0 0.000401
   10 8 0.000000 -0.874121 0 0.000568
   11 8 0.000000 -0.874121 10 0.000568
   12 8 0.000000 -0.874121 10 0.000568
   13 15 0.000000 1.295660 0 0.000385
   14 8 0.000000 -0.808153 0 0.000614
   15 8 0.000000 -0.808153 14 0.000614
   16 8 0.000000 -0.504444 0 0.000972
   17 15 0.000000 1.367824 0 0.000365
   18 8 0.000000 -0.838262 0 0.000592
   19 8 0.000000 -0.838262 18 0.000592
   20 8 0.000000 -0.547496 0 0.000898
   21 8 0.000000 -0.529450 0 0.000928
   22 6 0.000000 0.008818 0 0.004981
   23 1 0.000000 0.073118 0 0.000000
   24 1 0.000000 0.056336 0 0.000000
   25 1 0.000000 0.093358 0 0.000000
   26 12 0.000000 1.298719 0 0.000384
   27 6 0.000000 -0.509647 0 0.000963
   28 1 0.000000 0.177629 0 0.000000
   29 1 0.000000 0.153961 0 0.000000
   30 1 0.000000 0.091579 0 0.000000
   31 6 0.000000 0.983691 0 0.000506
   32 8 0.000000 -0.776470 0 0.000639
   33 7 0.000000 -0.950083 0 0.000523
   34 1 0.000000 0.429671 0 0.000000
   35 1 0.000000 0.429671 34 0.000000
   36 8 0.000000 -0.744648 0 0.000665
   37 1 0.000000 0.365327 0 0.000000
   38 1 0.000000 0.365327 37 0.000000
   39 6 0.000000 -0.469241 0 0.001042
   40 1 0.000000 0.057543 0 0.000000
   41 1 0.000000 0.052121 0 0.000000
   42 1 0.000000 0.153304 0 0.000000
   43 6 0.000000 0.941899 0 0.000528
   44 8 0.000000 -0.783262 0 0.000633
   45 8 0.000000 -0.783262 44 0.000633

 Sum over the calculated charges: -2.000

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
> ===============================================================
>
>
>

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