VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 07 2010 - 09:23:57 CST

Hi,
  Your PDB was line-wrapped (at least in my email program), so I can't
do anything useful with it.
It's always best to gzip things like PDB files for email, so that
the mail programs don't interpret them as text.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 06, 2010 at 01:50:06PM -0600, vani panguluri wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078