Dear Jiten,
several years ago, I developed force-field parameters for NADH, NAD+,
NADP+, and NADPH.
I do not know if they are good enough for you.
They are taken from the amber adenine and ribose input (residue RA5 in
all_nuc94.in) with the nicotinamide and pyrophosphate moieties added
using quantum chemically calculated charges with the RESP method and
RHF/6-31G* calculations. They are fully compatible to Amber 4.1 and
the Cornell et al. 1995 force field, but they can also be used with
later verions of Amber.
For NADPX, the charge of the 2'-phosphate group is not clear (pKa=6-7) so
two different molecules were developed, one with a total charge of -2
and the other with a total charge of -3.
It should be noted that Charmm22 force field parameters for NAD+ and
NADH were recently published: Paverlites et al, J. Comput. Chem. 18(97)
221-239. Their force constants and equilibrium values are probably
more accurate, whereas our charges are better and more compatible with
Amber.
I attach the PREP files for NAD+ and NADH.
Please, do not hesitate to contact me if you have any questions:
Ulf.Ryde.teokem.lu.se
Please, do not spread these parameters without informing me.
Best Regards,
Ulf
References:
NADH: U. Ryde, Proteins, Struct. Funct. Genet. 21(1995)40-50
"Molecular dynamic simulations of alcohol dehydrogenase
with varying coordination number of the catalytic zinc ion"
NAD+: U. Ryde, Prot. Sci. 4(1995)1124-1132
"On the role of Glu-68 in alcohol dehydrogenase"
NADP+: N. Holmberg, U. Ryde, and L. Bulow, Prot. Engin., 12 (1999) 851-856.
"Redesign of the coenzyme specificity in L-lactate dehydrogenase
from Bacillus stearothermophilus using site-directed mutagenesis
and media engineering."
Update:U. Ryde, "Force field parameters for NAD and NADP", manuscript
in preparation.
In addition to the prep files, the following parameters are also needed:
Special force constants for NAD+, NADH, NADP+, and NADPH; Ulf Ryde, 24
April, 1998
BOND
CA-N* 448.00 1.344 NAD: N1-C2 and N1-C6
ANGL
CA-C -O 80.00 119.80 NAD, Vanhommerig, BBA 1295(96)125
CA-C -N 70.00 115.70 NAD, Vanhommerig, BBA 1295(96)125
C -CA-CT 63.00 120.00 NAD
CA-CA-N* 70.00 119.50 NAD, Vanhommerig, BBA 1295(96)125
CT-CA-HA 35.00 120.00 NAD
H4-CA-N* 35.00 114.00 NAD
CA-CT-CA 63.00 120.00 NAD
CA-N*-CA 70.00 121.20 NAD, Vanhommerig, BBA 1295(96)125
CA-N*-CT 70.00 120.60 NAD, Vanhommerig, BBA 1295(96)125
DIHE
X -CA-N*-X 4 7.40 180.0 2. NAD;
=X-CM-N*-X
CA-CA-C -O 1 0.02 180.0 1. NAD,
Vanhommerig, BBA 1295(96)125
CA-CA-C -O 1 0.45 180.0 2. NAD,
Vanhommerig, BBA 1295(96)125
CA-CA-C -N 1 0.02 180.0 1. NAD,
Vanhommerig, BBA 1295(96)125
CA-CA-C -N 1 0.45 180.0 2. NAD,
Vanhommerig, BBA 1295(96)125
IMPR
CA-CA-N*-CT 1.0 180. 2. NAD
CA-CA-CA-C 1.1 180. 2. NAD
CA-CT-CA-C 1.1 180. 2. NAD
CT-CA-CA-C 1.1 180. 2. NAD
END
NAD+, AMBER 5.0 compatible; U. Ryde, to be published, 22/4-98
nad.dat
NAD INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 .000 .000 .000 .00000
2 DUMM DU M 1 0 -1 1.000 .000 .000 .00000
3 DUMM DU M 2 1 0 1.000 90.000 .000 .00000
4 C6N CA M 3 2 1 1.000 80.257 304.544 .05510
5 H6N H4 E 4 3 2 1.094 87.423 114.196 .20620
6 C5N CA M 4 3 2 1.403 39.816 260.797 -.26410
7 H5N HA E 6 4 3 1.082 118.946 321.661 .21020
8 C4N CA M 6 4 3 1.395 120.143 142.477 .13880
9 H4N HA E 8 6 4 1.088 119.134 178.384 .15800
10 C3N CA M 8 6 4 1.407 120.163 2.543 -.23450
11 C7N C B 10 8 6 1.505 119.504 173.166 .82170
12 O7N O E 11 10 8 1.233 117.812 21.930 -.54280
13 N7N N B 11 10 8 1.352 117.707 203.001 -.95200
14 H71 H E 13 11 10 1.008 120.000 179.793 .42270
15 H72 H E 13 11 10 1.013 120.000 1.300 .42270
16 C2N CA M 10 8 6 1.382 119.053 355.721 .03650
17 H2N H4 E 16 10 8 1.090 118.874 179.626 .15490
18 N1N N* M 16 10 8 1.387 120.593 1.805 .08310
19 C'N1 CT M 18 16 10 1.488 116.524 174.865 .32190
20 H'N1 H2 E 19 18 16 1.094 110.868 20.343 .07760
21 C'N2 CT M 19 18 16 1.508 117.258 142.452 .06700
22 H'N2 H1 E 21 19 18 1.087 113.425 45.778 .09720
23 O'N2 OH S 21 19 18 1.436 111.340 277.899 -.61390
24 HON2 HO E 23 21 19 .962 108.148 163.971 .41860
25 C'N3 CT M 21 19 18 1.520 99.733 162.298 .20220
26 H'N3 H1 E 25 21 19 1.091 114.726 198.145 .06150
27 O'N3 OH S 25 21 19 1.423 109.790 79.530 -.65410
28 HON3 HO E 27 25 21 .959 106.995 50.503 .43760
29 C'N4 CT M 25 21 19 1.521 103.900 322.360 .10650
30 H'N4 H1 E 29 25 21 1.091 111.525 142.478 .11740
31 O'N4 OS E 29 25 21 1.435 104.712 23.472 -.35480
32 C'N5 CT M 29 25 21 1.521 114.250 264.249 .05580
33 HN51 H1 E 32 29 25 1.029 113.342 288.300 .06790
34 HN52 H1 E 32 29 25 1.091 118.280 168.221 .06790
35 O'N5 OS M 32 29 25 1.440 108.747 48.875 -.56610
36 PN P M 35 32 29 1.620 117.474 190.938 1.37290
37 OPN1 O2 E 36 35 32 1.473 105.958 176.012 -.85580
38 OPN2 O2 E 36 35 32 1.481 109.032 308.271 -.85580
39 O3P OS M 36 35 32 1.574 100.139 62.417 -.57600
40 PA P M 39 36 35 1.611 136.620 195.390 1.37290
41 OPA1 O2 E 40 39 36 1.485 106.319 337.227 -.85580
42 OPA2 O2 E 40 39 36 1.477 109.295 207.094 -.85580
43 O'A5 OS M 40 39 36 1.580 103.587 92.769 -.56610
44 C'A5 CT M 43 40 39 1.420 121.317 75.897 .05580
45 HA51 H1 E 44 43 40 1.024 108.046 267.459 .06790
46 HA52 H1 E 44 43 40 1.093 115.908 35.989 .06790
47 C'A4 CT M 44 43 40 1.503 100.744 154.082 .10650
48 H'A4 H1 E 47 44 43 1.104 106.529 59.863 .11740
49 O'A4 OS E 47 44 43 1.414 106.546 175.953 -.35480
50 C'A3 CT M 47 44 43 1.523 112.631 292.482 .20220
51 H'A3 H1 E 50 47 44 1.092 111.048 -18.541 .06150
52 O'A3 OH S 50 47 44 1.434 110.551 135.535 -.65410
53 HOA3 HO E 52 50 47 .963 106.434 272.942 .43760
54 C'A2 CT M 50 47 44 1.511 103.289 252.113 .06700
55 H'A2 H1 E 54 50 47 1.091 107.136 88.678 .09720
56 O'A2 OH S 54 50 47 1.429 112.235 212.910 -.61390
57 HOA2 HO E 56 54 50 .961 108.137 20.616 .41860
58 C'A1 CT M 54 50 47 1.500 102.172 330.379 .03940
59 H'A1 H2 E 58 54 50 1.096 110.904 284.037 .20070
60 N9A N* M 58 54 50 1.481 115.254 161.267 -.02510
61 C8A CK M 60 58 54 1.339 126.756 321.228 .20060
62 H8A H5 E 61 60 58 1.081 125.157 359.651 .15530
63 N7A NB M 61 60 58 1.344 111.176 179.494 -.60730
64 C5A CB M 63 61 60 1.335 102.981 .509 .05150
65 C6A CA M 64 63 61 1.375 123.335 180.071 .70090
66 N6A N2 B 65 64 63 1.334 120.288 352.032 -.90190
67 H61 H E 66 65 64 1.001 123.199 184.201 .41150
68 H62 H E 66 65 64 1.004 122.265 4.217 .41150
69 N1A NC M 65 64 63 1.334 115.111 179.506 -.76150
70 C2A CQ M 69 65 64 1.345 122.289 359.037 .58750
71 H2A H5 E 70 69 65 1.079 119.198 180.231 .04730
72 N3A NC M 70 69 65 1.345 121.528 1.544 -.69970
73 C4A CB M 72 70 69 1.341 119.342 358.936 .30530
CHARGE NAD+
0.0551 0.2062 -0.2641 0.2102 0.1388
0.1580 -0.2345 0.8217 -0.5428 -0.9520
0.4227 0.4227 0.0365 0.1549 0.0831
0.3219 0.0776 0.0670 0.0972 -0.6139
0.4186 0.2022 0.0615 -0.6541 0.4376
0.1065 0.1174 -0.3548 0.0558 0.0679
0.0679 -0.5661 1.3729 -0.8558 -0.8558
-0.5760 1.3729 -0.8558 -0.8558 -0.5661
0.0558 0.0679 0.0679 0.1065 0.1174
-0.3548 0.2022 0.0615 -0.6541 0.4376
0.0670 0.0972 -0.6139 0.4186 0.0394
0.2007 -0.0251 0.2006 0.1553 -0.6073
0.0515 0.7009 -0.9019 0.4115 0.4115
-0.7615 0.5875 0.0473 -0.6997 0.3053
IMPROPER
C6N C2N N1N C'N1
N1N C3N C2N H2N
C2N C4N C3N C7N
C3N C5N C4N H4N
C4N C6N C5N H5N
C5N N1N C6N H6N
C3N N7N C7N O7N
C7N H71 N7N H72
C8A C4A N9A C'A1
C6A H61 N6A H62
N7A N9A C8A H8A
N1A N3A C2A H2A
C5A N1A C6A N6A
LOOP
N1N C6N
C'N1 O'N4
O'A4 C'A1
C4A C5A
C4A N9A
DONENADH, AMBER 5.0 compatible; U. Ryde, to be published, 22/4-98
nah.dat
NAH INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 .000 .000 .000 .00000
2 DUMM DU M 1 0 -1 1.000 .000 .000 .00000
3 DUMM DU M 2 1 0 1.000 90.000 .000 .00000
4 C6N CA M 3 2 1 1.000 80.257 304.544 -.35520
5 H6N H4 E 4 3 2 1.086 86.845 113.956 .22190
6 C5N CA M 4 3 2 1.403 39.816 260.797 -.17300
7 H5N HA E 6 4 3 1.080 118.831 322.829 .12570
8 C4N CT M 6 4 3 1.395 120.143 142.477 .13480
9 H41 HC E 8 6 4 1.093 106.309 122.831 .01960
10 H42 HC E 8 6 4 1.093 107.814 239.002 .01960
11 C3N CA M 8 6 4 1.407 120.163 2.543 -.22270
12 C7N C B 11 8 6 1.505 119.504 173.166 .82850
13 O7N O E 12 11 8 1.233 117.812 21.930 -.60990
14 N7N N B 12 11 8 1.352 117.707 203.001 -.99350
15 H71 H E 14 12 11 1.004 120.682 179.872 .40470
16 H72 H E 14 12 11 1.009 120.477 1.302 .40470
17 C2N CA M 11 8 6 1.382 119.053 355.721 -.18400
18 H2N H4 E 17 11 8 1.084 118.597 179.611 .14220
19 N1N N* M 17 11 8 1.387 120.593 1.805 .22930
20 C'N1 CT M 19 17 11 1.488 116.524 174.865 -.03840
21 H'N1 H2 E 20 19 17 1.094 110.618 20.227 .16170
22 C'N2 CT M 20 19 17 1.508 117.258 142.452 .06700
23 H'N2 H1 E 22 20 19 1.088 113.807 46.086 .09720
24 O'N2 OH S 22 20 19 1.436 111.340 277.899 -.61390
25 HON2 HO E 24 22 20 .959 106.795 89.056 .41860
26 C'N3 CT M 22 20 19 1.520 99.733 162.298 .20220
27 H'N3 H1 E 26 22 20 1.091 114.651 198.096 .06150
28 O'N3 OH S 26 22 20 1.423 109.790 79.530 -.65410
29 HON3 HO E 28 26 22 .960 105.431 40.651 .43760
30 C'N4 CT M 26 22 20 1.521 103.900 322.360 .10650
31 H'N4 H1 E 30 26 22 1.090 111.514 142.236 .11740
32 O'N4 OS E 30 26 22 1.435 104.712 23.472 -.35480
33 C'N5 CT M 30 26 22 1.521 114.250 264.249 .05580
34 HN51 H1 E 33 30 26 1.029 113.342 288.300 .06790
35 HN52 H1 E 33 30 26 1.092 118.256 168.168 .06790
36 O'N5 OS M 33 30 26 1.440 108.747 48.875 -.56610
37 PN P M 36 33 30 1.620 117.474 190.938 1.37290
38 OPN1 O2 E 37 36 33 1.473 105.958 176.012 -.85580
39 OPN2 O2 E 37 36 33 1.481 109.032 308.271 -.85580
40 O3P OS M 37 36 33 1.574 100.139 62.417 -.57600
41 PA P M 40 37 36 1.611 136.620 195.390 1.37290
42 OPA1 O2 E 41 40 37 1.485 106.319 337.227 -.85580
43 OPA2 O2 E 41 40 37 1.477 109.295 207.094 -.85580
44 O'A5 OS M 41 40 37 1.580 103.587 92.769 -.56610
45 C'A5 CT M 44 41 40 1.420 121.317 75.897 .05580
46 HA51 H1 E 45 44 41 1.024 108.046 267.459 .06790
47 HA52 H1 E 45 44 41 1.093 115.908 35.989 .06790
48 C'A4 CT M 45 44 41 1.503 100.744 154.082 .10650
49 H'A4 H1 E 48 45 44 1.104 106.529 59.863 .11740
50 O'A4 OS E 48 45 44 1.414 106.546 175.953 -.35480
51 C'A3 CT M 48 45 44 1.523 112.631 292.482 .20220
52 H'A3 H1 E 51 48 45 1.092 111.048 -18.541 .06150
53 O'A3 OH S 51 48 45 1.434 110.551 135.535 -.65410
54 HOA3 HO E 53 51 48 .962 106.326 273.873 .43760
55 C'A2 CT M 51 48 45 1.511 103.289 252.113 .06700
56 H'A2 H1 E 55 51 48 1.091 107.136 88.678 .09720
57 O'A2 OH S 55 51 48 1.429 112.235 212.910 -.61390
58 HOA2 HO E 57 55 51 .961 108.105 20.361 .41860
59 C'A1 CT M 55 51 48 1.500 102.172 330.379 .03940
60 H'A1 H2 E 59 55 51 1.096 110.904 284.037 .20070
61 N9A N* M 59 55 51 1.481 115.254 161.267 -.02510
62 C8A CK M 61 59 55 1.339 126.756 321.228 .20060
63 H8A H5 E 62 61 59 1.081 125.157 359.651 .15530
64 N7A NB M 62 61 59 1.344 111.176 179.494 -.60730
65 C5A CB M 64 62 61 1.335 102.981 .509 .05150
66 C6A CA M 65 64 62 1.375 123.335 180.071 .70090
67 N6A N2 B 66 65 64 1.334 120.288 352.032 -.90190
68 H61 H E 67 66 65 1.001 123.250 184.224 .41150
69 H62 H E 67 66 65 1.004 122.140 3.982 .41150
70 N1A NC M 66 65 64 1.334 115.111 179.506 -.76150
71 C2A CQ M 70 66 65 1.345 122.289 359.037 .58750
72 H2A H5 E 71 70 66 1.079 119.198 180.231 .04730
73 N3A NC M 71 70 66 1.345 121.528 1.544 -.69970
74 C4A CB M 73 71 70 1.341 119.342 358.936 .30530
CHARGE NADH
-0.3552 0.2219 -0.1730 0.1257 0.1348
0.0196 0.0196 -0.2227 0.8285 -0.6099
-0.9935 0.4047 0.4047 -0.1840 0.1422
0.2293 -0.0384 0.1617 0.0670 0.0972
-0.6139 0.4186 0.2022 0.0615 -0.6541
0.4376 0.1065 0.1174 -0.3548 0.0558
0.0679 0.0679 -0.5661 1.3729 -0.8558
-0.8558 -0.5760 1.3729 -0.8558 -0.8558
-0.5661 0.0558 0.0679 0.0679 0.1065
0.1174 -0.3548 0.2022 0.0615 -0.6541
0.4376 0.0670 0.0972 -0.6139 0.4186
0.0394 0.2007 -0.0251 0.2006 0.1553
-0.6073 0.0515 0.7009 -0.9019 0.4115
0.4115 -0.7615 0.5875 0.0473 -0.6997
0.3053
IMPROPER
C6N C2N N1N C'N1
N1N C3N C2N H2N
C2N C4N C3N C7N
C4N C6N C5N H5N
C5N N1N C6N H6N
C3N N7N C7N O7N
C7N H71 N7N H72
C8A C4A N9A C'A1
C6A H61 N6A H62
N7A N9A C8A H8A
N1A N3A C2A H2A
C5A N1A C6A N6A
LOOP
N1N C6N
C'N1 O'N4
O'A4 C'A1
C4A C5A
C4A N9A
DONE
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Received on Wed Jan 14 2004 - 15:53:05 PST
