Date sent: Mon, 08 Dec 2003 12:05:25 +0100 From: Ulf Ryde To: amber@scripps.edu Subject: Re: AMBER: NAD+ and NADH amber parameters Send reply to: amber@scripps.edu 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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber@scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo@scripps.edu