VMD-L Mailing List

From: vani panguluri (vanipanguluri_at_gmail.com)
Date: Mon Dec 06 2010 - 13:50:06 CST

Hello,

I had used these two pdb files but i am unable to generate the psf file for
apocynin i am giving the information about apocynin.pdb below can anyone
suggest me a solution to do this.one more question could we able to perform
the namd simulation by merging a chemical and protein and the apocynin which
i mentioned above was a chemical.

HEADER CSD ENTRY I
CRYST1 8.5144 8.7780 10.7120 90.00 90.08 90.00 P21/n
SCALE1 0.117448 0.000000 0.000168 0.000000
SCALE2 0.000000 0.113921 0.000000 0.000000
SCALE3 0.000000 0.000000 0.093353 0.000000
HETATM 1 O1 UNK 1 4.713 6.641 7.659 1.00 1.92
O
ANISOU 1 O1 UNK 1 225 146 357 -6 -127 14
O
HETATM 2 O2 UNK 1 2.367 6.156 6.453 1.00 1.71
O
ANISOU 2 O2 UNK 1 165 160 326 52 -105 -24
O
HETATM 3 O3 UNK 1 4.047 0.395 7.123 1.00 2.24
O
ANISOU 3 O3 UNK 1 276 162 411 32 -89 6
O
HETATM 4 C1 UNK 1 4.350 5.366 7.385 1.00 1.31
C
ANISOU 4 C1 UNK 1 153 167 178 -13 -22 11
C
HETATM 5 C2 UNK 1 3.131 5.058 6.758 1.00 1.24
C
ANISOU 5 C2 UNK 1 140 168 162 40 -10 7
C
HETATM 6 C3 UNK 1 2.795 3.742 6.509 1.00 1.29
C
ANISOU 6 C3 UNK 1 138 181 172 -2 -21 -9
C
HETATM 7 C4 UNK 1 3.664 2.707 6.891 1.00 1.31
C
ANISOU 7 C4 UNK 1 164 161 174 9 0 17
C
HETATM 8 C5 UNK 1 4.864 3.021 7.512 1.00 1.50
C
ANISOU 8 C5 UNK 1 158 181 230 18 -28 56
C
HETATM 9 C6 UNK 1 5.209 4.340 7.753 1.00 1.51
C
ANISOU 9 C6 UNK 1 148 201 224 -13 -48 45
C
HETATM 10 C7 UNK 1 1.116 5.909 5.803 1.00 1.92
C
ANISOU 10 C7 UNK 1 179 225 327 52 -106 -12
C
HETATM 11 C8 UNK 1 3.326 1.278 6.662 1.00 1.53
C
ANISOU 11 C8 UNK 1 189 181 212 -3 11 5
C
HETATM 12 C9 UNK 1 2.112 0.915 5.869 1.00 2.04
C
ANISOU 12 C9 UNK 1 261 215 299 -41 -71 3
C
HETATM 13 H1 UNK 1 4.170 7.198 7.402 1.00 5.68
H
HETATM 14 H3 UNK 1 1.947 3.530 6.067 1.00 1.50
H
HETATM 15 H5 UNK 1 5.472 2.302 7.785 1.00 1.74
H
HETATM 16 H6 UNK 1 6.063 4.550 8.184 1.00 1.82
H
HETATM 17 H7A UNK 1 1.274 5.456 4.950 1.00 2.29
H
HETATM 18 H7C UNK 1 0.556 5.343 6.376 1.00 2.29
H
HETATM 19 H9B UNK 1 2.137 1.375 5.004 1.00 2.45
H
HETATM 20 H9C UNK 1 1.309 1.187 6.360 1.00 2.45
H
HETATM 21 H9A UNK 1 2.093 -0.054 5.723 1.00 2.45
H
HETATM 22 HB UNK 1 0.659 6.761 5.641 1.00 2.29
Unknown
CONECT 1 4 13
CONECT 2 5 10
CONECT 3 11
CONECT 4 1 5 9
CONECT 5 2 4 6
CONECT 6 5 7 14
CONECT 7 6 8 11
CONECT 8 7 9 15
CONECT 9 4 8 16
CONECT 10 2 17 18
CONECT 11 3 7 12
CONECT 12 11 19 20 21
CONECT 13 1
CONECT 14 6
CONECT 15 8
CONECT 16 9
CONECT 17 10
CONECT 18 10
CONECT 19 12
CONECT 20 12
CONECT 21 12
CONECT 22
MASTER 0 0 0 0 0 0 0 3 22 0 22 0
END

Can Anyone suggest me a solution.sorry if i am troubling anyone.

Thanks & Regards,
Vani Pangluri