Re: NADP problem

From: Hemant Kushwaha (hemant.kushwaha_at_gmail.com)
Date: Fri Jun 03 2005 - 22:07:08 CDT

Hi all,

I am trying to build psf file with NADP present within the structure,
but I have noticed that while adding hydrogen to the NADP structure
psfgen is making some weird contacts and even hydrogen os not visible
in the pdb file seen in VMD.....

It was said earlier that it is the topology problem, but i am not able
to find out what exactly is wrong in the topology file........

Can anyone help me in finding out what is wrong with the the topology file.

RESI NADP -2.00 ! oxidized nicotinamide adenine dinucleotide,
                        ! NADP+, adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params,
adm jr., 9/98
                        ! note that differences with respect to
published results exist
                        ! due to new NA params
                        !
GROUP !
ATOM AC4' CN7 0.16 ! AH61 AH62
ATOM AH4' HN7 0.09 ! \ /
ATOM AO4' ON6B -0.50 ! AN6
ATOM AC1' CN7B 0.16 ! |
ATOM AH1' HN7 0.09 ! AC6
GROUP ! // \
ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\
ATOM AN7 NN4 -0.71 ! | || AC8-AH8
ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/
ATOM AH8 HN3 0.12 ! / \\ / \
ATOM AN9 NN2 -0.05 ! AH2 AN3 \
                        ! \
ATOM AN1 NN3A -0.74 ! \
ATOM AC2 CN4 0.50 ! \
ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \
ATOM AN3 NN3A -0.75 ! | | | \ / \ \
ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1'
ATOM AC6 CN2 0.46 ! \ | | | \ / \
                        ! \ NO2 AO2 AH5' AC3'-AC2' AH1'
ATOM AN6 NN1 -0.77 ! \ / \ / \
ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2'
ATOM AH62 HN1 0.38 ! \ | |
GROUP ! \ AH3T AO1P=AP2==AO2P (-)
ATOM AC2' CN7B 0.01 ! \ | NH71
ATOM AH2' HN7 0.09 ! \ AH2T-AO2T /
ATOM AO2' ON2 -0.62 ! \ NH72-NN7 NH4 NH42
ATOM AP2 P 1.50 ! \ \ \ /
ATOM AO1P ON3 -0.82 ! \ NC7 NC4
ATOM AO2P ON3 -0.82 ! \ / \ / \
ATOM AO2T ON4 -0.68 ! \ NO7 NC3 NC5-NH5
ATOM AH2T HN4 0.34 ! \ | |
GROUP ! \ | |
ATOM AC3' CN7 0.14 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6
ATOM AH3' HN7 0.09 ! \ | \ / \ \ /
ATOM AO3' ON5 -0.66 ! NC5'--NC4' NC1'--------NN1
ATOM AH3T HN5 0.43 ! | \ / \
GROUP ! NH5' NC3'-NC2'NH1'
ATOM AC5' CN8B -0.08 ! / \ / \
ATOM AH5' HN8 0.09 ! NO3' NH3'NO2'NH2'
ATOM AH5s HN8 0.09 ! | |
ATOM AP P 1.50 ! NH3T NH2T
ATOM AO1 ON3 -0.82 !
ATOM AO2 ON3 -0.82 !
ATOM AO5' ON2 -0.62 !
ATOM O3 ON2 -0.68
ATOM NP P 1.50
ATOM NO1 ON3 -0.82
ATOM NO2 ON3 -0.82
ATOM NO5' ON2 -0.62
ATOM NC5' CN8B -0.08
ATOM NH5s HN8 0.09
ATOM NH5' HN8 0.09
GROUP
ATOM NC2' CN7B 0.14
ATOM NH2' HN7 0.09
ATOM NO2' ON5 -0.66
ATOM NH2T HN5 0.43
GROUP
ATOM NC3' CN7 0.14
ATOM NH3' HN7 0.09
ATOM NO3' ON5 -0.66
ATOM NH3T HN5 0.43
GROUP
ATOM NC1' CN7B 0.16
ATOM NH1' HN7 0.09
ATOM NC4' CN7 0.16
ATOM NH4' HN7 0.09
ATOM NO4' ON6B -0.50
GROUP
ATOM NN1 NN2 -0.07
ATOM NC6 CN3B 0.16
ATOM NH6 HN3B 0.19
ATOM NC5 CN3 -0.10
ATOM NH5 HN3B 0.16
ATOM NC4 CN3A -0.05
ATOM NH4 HN3B 0.16
ATOM NC3 CN3 0.05
ATOM NC2 CN3B 0.18
ATOM NH2 HN3B 0.16
ATOM NC7 CN1A 0.68
ATOM NO7 ON1 -0.40
ATOM NN7 NN1 -0.82
ATOM NH71 HN1 0.34 ! trans to amide O
ATOM NH72 HN1 0.36 ! cis to amide O

BOND AN1 AC2 AN3 AC4 AC5 AC6
BOND AC6 AN6 AC5 AN7 AC8 AN9 AC6 AN1 AN7 AC8
BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8
DOUBLE AC2 AN3 AC4 AC5
BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4'
DOUBLE AP2 AO1P AP AO1 NP NO1
BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2'
BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5'
BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP
DOUBLE AP AO1 NP NO1
BOND AP AO2 AP O3 O3 NP NP NO2
BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4'
BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4'
BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3'
BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2
BOND NC3 NC4 NC5 NC6
BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71
BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6
BOND AP2 AO2P AP2 AO2T AO2T AH2T
DOUBLE NC2 NC3 NC4 NC5 NC6 NN1
! adenine impropers
IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6
! amide impropers
IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7
IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71
! ring hydrogen impropers
IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5
IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1 AP
ACCE AO2 AP
ACCE O3
ACCE NO1 NP
ACCE NO2 NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2'
IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977
IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863
IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836
IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942
IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756
IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636
IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491
IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232
IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942
IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337
IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942
IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491
IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337
IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415
IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847
IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013
IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777
IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282
IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782
IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146
IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482
IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300
IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648
IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419
IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912
IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978
IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419
IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912
IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978
IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962
IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928
IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294
IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097
IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097
IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105
IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999
IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110
IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000
IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111
IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111
IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636
IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977
IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977
IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160
IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160
IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160
IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270
IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100
IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712
IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100
IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270
IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110
IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110
IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110
IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110
IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110
IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110
IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800
IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270
IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160
IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150
IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500
IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600
IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600
IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500
IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199
IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150
IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800
IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300
IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600
IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000
IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000
IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900
IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900
IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900
IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900
IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000
IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000
IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000
IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000
IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000
PATCH FIRST NONE LAST NONE
END

I will be very thankful for anyone's kind help.

Regards
hemant


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