AMBER Archive (2003)

Subject: Re: AMBER: NAD+ and NADH amber parameters

From: Ulf Ryde (ulf.ryde_at_teokem.lu.se)
Date: Mon Dec 08 2003 - 05:05:25 CST

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_at_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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