AMBER Archive (2003)

Subject: Re: AMBER: RESP charges

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Thu Dec 18 2003 - 17:31:51 CST

Thanks, Junmei:
  Yeap. You are right. The second step didn't work acturally. Because I
followed the instructions on the AMBER7 maual Page78, which has errors in that
part, I also made mistakes sequentially. I generated the resp charges for the
2nd step fitting after correcting the errors. I pasted the output files from
the 1st and 2nd fitting here. In addition, do you think the resp charges I
got for a Mg2+ coordination system are reasonable? And the default resp input
file settings are good enough?

Thanks again.
Have a nice evening!

Youyi Peng

resp step1 output
---------------------------------------------
      Restrained ESP Fit 2.3 Amber 4.1
 -----------------------------------------------
 Resp charges for organic molecule
 -----------------------------------------------

 inopt = 0 ioutopt = 1
 nmol = 1 iqopt = 0
 ihfree = 1 irstrnt = 1
 iunits = 0 qwt = 0.00050000
 wtmol(1) = 1.000000
 subtitle:

Resp charges for organic molecule
ich = -2 iuniq = 45
    1 6 0
    2 1 0
    3 1 0
    4 1 0
    5 7 0
    6 1 0
    7 1 6
    8 1 6
    9 15 0
   10 8 0
   11 8 10
   12 8 10
   13 15 0
   14 8 0
   15 8 14
   16 8 0
   17 15 0
   18 8 0
   19 8 18
   20 8 0
   21 8 0
   22 6 0
   23 1 0
   24 1 0
   25 1 0
   26 12 0
   27 6 0
   28 1 0
   29 1 0
   30 1 0
   31 6 0
   32 8 0
   33 7 0
   34 1 0
   35 1 34
   36 8 0
   37 1 0
   38 1 37
   39 6 0
   40 1 0
   41 1 0
   42 1 0
   43 6 0
   44 8 0
   45 8 44

  ----------------------------------------------------------------------------

     ATOM COORDINATES CHARGE
                       X Y Z
  ----------------------------------------------------------------------------

  ----------------------------------------------------------------------------

 Charge on the molecule(ich) = -2
 Total number of atoms (iuniq) = 45
 Weight factor on initial charge restraints(qwt)= 0.50000E-03

  there are 1 charge constraints:

     1 1
     2 1
     3 1
     4 1
     5 1
     6 1
     7 1
     8 1
     9 1
    10 1
    11 1
    12 1
    13 1
    14 1
    15 1
    16 1
    17 1
    18 1
    19 1
    20 1
    21 1
    22 1
    23 1
    24 1
    25 1
    26 1
    27 1
    28 1
    29 1
    30 1
    31 1
    32 1
    33 1
    34 1
    35 1
    36 1
    37 1
    38 1
    39 1
    40 1
    41 1
    42 1
    43 1
    44 1
    45 1

 Reading esp"s for molecule 1
 total number of atoms = 45
 total number of esp points = 31012

 center X Y Z
    1 -0.8888175E+01 -0.4095741E+01 -0.2395634E+01
    2 -0.9785920E+01 -0.5431745E+01 -0.1110310E+01
    3 -0.8825266E+01 -0.2206915E+01 -0.1576374E+01
    4 -0.9826311E+01 -0.4057174E+01 -0.4228919E+01
    5 -0.6272609E+01 -0.4933171E+01 -0.2798575E+01
    6 -0.5372317E+01 -0.3695892E+01 -0.4001546E+01
    7 -0.5334638E+01 -0.4977355E+01 -0.1093615E+01
    8 -0.6274234E+01 -0.6714340E+01 -0.3583618E+01
    9 0.1098405E+01 0.4668906E+01 -0.1386621E+01
   10 0.3174929E-01 0.7322853E+01 -0.1151051E+01
   11 0.3904420E+01 0.4314524E+01 -0.9423591E+00
   12 0.6716937E+00 0.4153314E+01 -0.4272973E+01
   13 -0.3530877E+01 0.2346690E+01 -0.6725629E+00
   14 -0.4831226E+01 0.4411873E+01 0.7158566E+00
   15 -0.4084221E+01 0.2307520E+01 -0.3306625E+01
   16 -0.6351426E+00 0.2716995E+01 0.1523951E+00
   17 -0.2745980E+01 -0.2054264E+01 0.2393903E+01
   18 -0.3083080E+01 -0.4754284E+01 0.1881477E+01
   19 0.9966037E-01 -0.1601008E+01 0.2564373E+01
   20 -0.4230823E+01 -0.3365319E+00 0.5087879E+00
   21 -0.3529596E+01 -0.1152463E+01 0.5155356E+01
   22 -0.3531042E+01 0.1161717E+01 0.6535889E+01
   23 -0.2854357E+01 0.7995846E+00 0.8447436E+01
   24 -0.5452058E+01 0.1902130E+01 0.6596667E+01
   25 -0.2287547E+01 0.2504424E+01 0.5590584E+01
   26 0.2697079E+01 0.5333355E+00 0.5732087E+00
   27 0.9187800E+01 -0.4109916E+01 0.1825366E+01
   28 0.8661701E+01 -0.4236909E+01 0.3812736E+01
   29 0.8642316E+01 -0.5825471E+01 0.8241983E+00
   30 0.1120955E+02 -0.3816931E+01 0.1562015E+01
   31 0.7771897E+01 -0.1865377E+01 0.6414372E+00
   32 0.5865778E+01 -0.1146449E+01 0.1778603E+01
   33 0.8422528E+01 -0.8713508E+00 -0.1645910E+01
   34 0.1002140E+02 -0.1499700E+01 -0.2560907E+01
   35 0.7314865E+01 0.5077070E+00 -0.2458303E+01
   36 0.2869834E+01 0.2853972E+01 0.3876860E+01
   37 0.4038445E+01 0.1353609E+01 0.3462371E+01
   38 0.1269142E+01 0.2202663E+01 0.4772367E+01
   39 0.2932980E+01 -0.5275646E+01 -0.1375756E+01
   40 0.2198513E+01 -0.7093088E+01 -0.2008493E+01
   41 0.4991407E+01 -0.5304805E+01 -0.1445119E+01
   42 0.2316239E+01 -0.4920338E+01 0.5571989E+00
   43 0.1952705E+01 -0.3206735E+01 -0.3082859E+01
   44 0.5952750E+00 -0.3824116E+01 -0.4905942E+01
   45 0.2487490E+01 -0.9321470E+00 -0.2709379E+01
 Initial ssvpot = 1136.206

 Number of unique UNfrozen centers= 36

 Non-linear optimization requested.
 qchnge = 0.9781267525E-01
 qchnge = 0.4818923415E-03
 qchnge = 0.2302629352E-04
 qchnge = 0.1235857240E-05

 Convergence in 3 iterations

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

        Statistics of the fitting:
  The initial sum of squares (ssvpot) 1136.206
  The residual sum of squares (chipot) 0.118
  The std err of estimate (sqrt(chipot/N)) 0.00195
  ESP relative RMS (SQRT(chipot/ssvpot)) 0.01018

 Center of Mass (Angst.):

 X = 0.00000 Y = 0.00000 Z = 0.00000

 Dipole (Debye):

 X = 1.93597 Y = -28.02887 Z = 9.70646

 Dipole Moment (Debye)= 29.72509

 Quadrupole (Debye*Angst.):

 Qxx = 212.13080 QYY =-178.94038 QZZ = -33.19041
 Qxy = 154.75448 QXZ = 139.33206 QYZ = 212.14608

respout2
-----------------------------------------------
      Restrained ESP Fit 2.3 Amber 4.1
 -----------------------------------------------
 Resp charges for organic molecule
 -----------------------------------------------

 inopt = 0 ioutopt = 1
 nmol = 1 iqopt = 2
 ihfree = 1 irstrnt = 1
 iunits = 0 qwt = 0.00100000
 wtmol(1) = 1.000000
 subtitle:

Resp charges for organic molecule
ich = -2 iuniq = 45
    1 6 0
    2 1 0
    3 1 2
    4 1 2
    5 7 -99
    6 1 -99
    7 1 -99
    8 1 -99
    9 15 -99
   10 8 -99
   11 8 -99
   12 8 -99
   13 15 -99
   14 8 -99
   15 8 -99
   16 8 -99
   17 15 -99
   18 8 -99
   19 8 -99
   20 8 -99
   21 8 -99
   22 6 0
   23 1 0
   24 1 23
   25 1 23
   26 12 -99
   27 6 0
   28 1 0
   29 1 28
   30 1 28
   31 6 -99
   32 8 -99
   33 7 -99
   34 1 -99
   35 1 -99
   36 8 -99
   37 1 -99
   38 1 -99
   39 6 0
   40 1 0
   41 1 40
   42 1 40
   43 6 -99
   44 8 -99
   45 8 -99
 new q0 values to be read 45

  ----------------------------------------------------------------------------

     ATOM COORDINATES CHARGE
                       X Y Z
  ----------------------------------------------------------------------------

  ----------------------------------------------------------------------------

 Charge on the molecule(ich) = -2
 Total number of atoms (iuniq) = 45
 Weight factor on initial charge restraints(qwt)= 0.10000E-02

  there are 1 charge constraints:

     1 1
     2 1
     3 1
     4 1
     5 1
     6 1
     7 1
     8 1
     9 1
    10 1
    11 1
    12 1
    13 1
    14 1
    15 1
    16 1
    17 1
    18 1
    19 1
    20 1
    21 1
    22 1
    23 1
    24 1
    25 1
    26 1
    27 1
    28 1
    29 1
    30 1
    31 1
    32 1
    33 1
    34 1
    35 1
    36 1
    37 1
    38 1
    39 1
    40 1
    41 1
    42 1
    43 1
    44 1
    45 1

 Reading esp"s for molecule 1
 total number of atoms = 45
 total number of esp points = 31012

 center X Y Z
    1 -0.8888175E+01 -0.4095741E+01 -0.2395634E+01
    2 -0.9785920E+01 -0.5431745E+01 -0.1110310E+01
    3 -0.8825266E+01 -0.2206915E+01 -0.1576374E+01
    4 -0.9826311E+01 -0.4057174E+01 -0.4228919E+01
    5 -0.6272609E+01 -0.4933171E+01 -0.2798575E+01
    6 -0.5372317E+01 -0.3695892E+01 -0.4001546E+01
    7 -0.5334638E+01 -0.4977355E+01 -0.1093615E+01
    8 -0.6274234E+01 -0.6714340E+01 -0.3583618E+01
    9 0.1098405E+01 0.4668906E+01 -0.1386621E+01
   10 0.3174929E-01 0.7322853E+01 -0.1151051E+01
   11 0.3904420E+01 0.4314524E+01 -0.9423591E+00
   12 0.6716937E+00 0.4153314E+01 -0.4272973E+01
   13 -0.3530877E+01 0.2346690E+01 -0.6725629E+00
   14 -0.4831226E+01 0.4411873E+01 0.7158566E+00
   15 -0.4084221E+01 0.2307520E+01 -0.3306625E+01
   16 -0.6351426E+00 0.2716995E+01 0.1523951E+00
   17 -0.2745980E+01 -0.2054264E+01 0.2393903E+01
   18 -0.3083080E+01 -0.4754284E+01 0.1881477E+01
   19 0.9966037E-01 -0.1601008E+01 0.2564373E+01
   20 -0.4230823E+01 -0.3365319E+00 0.5087879E+00
   21 -0.3529596E+01 -0.1152463E+01 0.5155356E+01
   22 -0.3531042E+01 0.1161717E+01 0.6535889E+01
   23 -0.2854357E+01 0.7995846E+00 0.8447436E+01
   24 -0.5452058E+01 0.1902130E+01 0.6596667E+01
   25 -0.2287547E+01 0.2504424E+01 0.5590584E+01
   26 0.2697079E+01 0.5333355E+00 0.5732087E+00
   27 0.9187800E+01 -0.4109916E+01 0.1825366E+01
   28 0.8661701E+01 -0.4236909E+01 0.3812736E+01
   29 0.8642316E+01 -0.5825471E+01 0.8241983E+00
   30 0.1120955E+02 -0.3816931E+01 0.1562015E+01
   31 0.7771897E+01 -0.1865377E+01 0.6414372E+00
   32 0.5865778E+01 -0.1146449E+01 0.1778603E+01
   33 0.8422528E+01 -0.8713508E+00 -0.1645910E+01
   34 0.1002140E+02 -0.1499700E+01 -0.2560907E+01
   35 0.7314865E+01 0.5077070E+00 -0.2458303E+01
   36 0.2869834E+01 0.2853972E+01 0.3876860E+01
   37 0.4038445E+01 0.1353609E+01 0.3462371E+01
   38 0.1269142E+01 0.2202663E+01 0.4772367E+01
   39 0.2932980E+01 -0.5275646E+01 -0.1375756E+01
   40 0.2198513E+01 -0.7093088E+01 -0.2008493E+01
   41 0.4991407E+01 -0.5304805E+01 -0.1445119E+01
   42 0.2316239E+01 -0.4920338E+01 0.5571989E+00
   43 0.1952705E+01 -0.3206735E+01 -0.3082859E+01
   44 0.5952750E+00 -0.3824116E+01 -0.4905942E+01
   45 0.2487490E+01 -0.9321470E+00 -0.2709379E+01
 Initial ssvpot = 1136.206

 Number of unique UNfrozen centers= 8

 Non-linear optimization requested.
 qchnge = 0.9777354575E-01
 qchnge = 0.6447081776E-04
 qchnge = 0.4797294791E-06

 Convergence in 2 iterations

Resp charges for organic molecule

          Point Charges Before & After Optimization

    no. At.no. q(init) q(opt) ivary d(rstr)/dq
    1 6 -0.002792 -0.023304 0 0.009739
    2 1 0.031850 0.070352 0 0.000000
    3 1 0.115049 0.070352 2 0.000000
    4 1 0.055049 0.070352 2 0.000000
    5 7 -0.210419 -0.210419 -99 0.004292
    6 1 0.295469 0.295469 -99 0.000000
    7 1 0.295469 0.295469 -99 0.000000
    8 1 0.295469 0.295469 -99 0.000000
    9 15 1.242491 1.242491 -99 0.000802
   10 8 -0.874121 -0.874121 -99 0.001137
   11 8 -0.874121 -0.874121 -99 0.001137
   12 8 -0.874121 -0.874121 -99 0.001137
   13 15 1.295660 1.295660 -99 0.000770
   14 8 -0.808153 -0.808153 -99 0.001228
   15 8 -0.808153 -0.808153 -99 0.001228
   16 8 -0.504444 -0.504444 -99 0.001945
   17 15 1.367824 1.367824 -99 0.000729
   18 8 -0.838262 -0.838262 -99 0.001185
   19 8 -0.838262 -0.838262 -99 0.001185
   20 8 -0.547496 -0.547496 -99 0.001797
   21 8 -0.529450 -0.529450 -99 0.001856
   22 6 0.008818 0.152693 0 0.005478
   23 1 0.073118 0.034893 0 0.000000
   24 1 0.056336 0.034893 23 0.000000
   25 1 0.093358 0.034893 23 0.000000
   26 12 1.298719 1.298719 -99 0.000768
   27 6 -0.509647 -0.453163 0 0.002155
   28 1 0.177629 0.120047 0 0.000000
   29 1 0.153961 0.120047 28 0.000000
   30 1 0.091579 0.120047 28 0.000000
   31 6 0.983691 0.983691 -99 0.001011
   32 8 -0.776470 -0.776470 -99 0.001277
   33 7 -0.950083 -0.950083 -99 0.001047
   34 1 0.429671 0.429671 -99 0.000000
   35 1 0.429671 0.429671 -99 0.000000
   36 8 -0.744648 -0.744648 -99 0.001331
   37 1 0.365327 0.365327 -99 0.000000
   38 1 0.365327 0.365327 -99 0.000000
   39 6 -0.469241 -0.565676 0 0.001741
   40 1 0.057543 0.117204 0 0.000000
   41 1 0.052121 0.117204 40 0.000000
   42 1 0.153304 0.117204 40 0.000000
   43 6 0.941899 0.941899 -99 0.001056
   44 8 -0.783262 -0.783262 -99 0.001266
   45 8 -0.783262 -0.783262 -99 0.001266

 Sum over the calculated charges: -2.000

        Statistics of the fitting:
  The initial sum of squares (ssvpot) 1136.206
  The residual sum of squares (chipot) 0.261
  The std err of estimate (sqrt(chipot/N)) 0.00290
  ESP relative RMS (SQRT(chipot/ssvpot)) 0.01515

 Center of Mass (Angst.):

 X = 0.00000 Y = 0.00000 Z = 0.00000

 Dipole (Debye):

 X = 2.03039 Y = -28.33523 Z = 9.60483

 Dipole Moment (Debye)= 29.98768

 Quadrupole (Debye*Angst.):

 Qxx = 218.34500 QYY =-180.67498 QZZ = -37.67002
 Qxy = 152.22291 QXZ = 125.56109 QYZ = 210.90056

Junmei Wang wrote:

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

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