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.tbc.com
> Homepage: Http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
> ===============================================================
>
>
>
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Received on Wed Jan 14 2004 - 15:53:11 PST
