VMD-L Mailing List

From: Jernej Zidar (jernej.zidar_at_gmail.com)
Date: Thu Aug 02 2012 - 04:31:10 CDT

You are missing residues 24 and 25. That's the problem. IMO.

*J*

On Thu, Aug 2, 2012 at 2:36 AM, MeiShan Lin <stylelim_at_gmail.com> wrote:
> I have a weird problem while I am generating the side chain atoms from its
> backbone coordinate by using automatic psf builder.
> My input PDB file only contains the coordinates of backbone of each residue,
> ex:
> ATOM 65 N GLN Z 23 67.637 -15.852 -2.478 1.00 30.00
> ATOM 66 CA GLN Z 23 66.733 -16.285 -1.593 1.00 30.00
> ATOM 67 C GLN Z 23 67.338 -16.110 -0.213 1.00 30.00
> ATOM 68 O GLN Z 23 66.677 -15.703 0.668 1.00 30.00
> ATOM 69 N TYR Z 26 68.587 -16.423 -0.020 1.00 30.00
> ATOM 70 CA TYR Z 26 69.928 -16.256 1.993 1.00 30.00
> ATOM 71 C TYR Z 26 71.235 -16.682 1.386 1.00 30.00
> ATOM 72 O TYR Z 26 71.665 -17.632 1.671 1.00 30.00
> ATOM 73 N ALA Z 27 71.848 -16.000 0.536 1.00 30.00
> ATOM 74 CA ALA Z 27 72.690 -16.352 -0.465 1.00 30.00
> ATOM 75 C ALA Z 27 73.478 -15.410 -1.347 1.00 30.00
> ATOM 76 O ALA Z 27 73.078 -14.318 -1.575 1.00 30.00
>
>
> After I generate psf file by using automatic PSF builder, some of the
> residues are missing, (here, I am missing Tyr (Res26))
>
> part of my autopsf.pdb file is as following:
> ATOM 239 C GLN Z 23 67.338 -16.110 -0.213 1.00 0.00 P2
> C
> ATOM 240 OT1 GLN Z 23 68.253 -15.718 -0.306 0.00 0.00 P2
> O
> ATOM 241 OT2 GLN Z 23 66.682 -16.427 0.472 0.00 0.00 P2
> O
> ATOM 242 N GLN Z 23 67.637 -15.852 -2.478 1.00 0.00 P2
> N
> ATOM 243 HN GLN Z 23 67.659 -16.368 -3.332 0.00 0.00 P2
> H
> ATOM 244 CA GLN Z 23 66.733 -16.285 -1.593 1.00 0.00 P2
> C
> ATOM 245 HA GLN Z 23 65.858 -15.649 -1.649 0.00 0.00 P2
> H
> ATOM 246 CB GLN Z 23 66.346 -17.765 -1.867 0.00 0.00 P2
> C
> ATOM 247 HB1 GLN Z 23 65.936 -17.804 -2.902 0.00 0.00 P2
> H
> ATOM 248 HB2 GLN Z 23 67.267 -18.392 -1.873 0.00 0.00 P2
> H
> ATOM 249 CG GLN Z 23 65.298 -18.373 -0.894 0.00 0.00 P2
> C
> ATOM 250 HG1 GLN Z 23 65.687 -18.369 0.146 0.00 0.00 P2
> H
> ATOM 251 HG2 GLN Z 23 64.359 -17.783 -0.909 0.00 0.00 P2
> H
> ATOM 252 CD GLN Z 23 64.968 -19.832 -1.227 0.00 0.00 P2
> C
> ATOM 253 OE1 GLN Z 23 64.157 -20.475 -0.562 0.00 0.00 P2
> O
> ATOM 254 NE2 GLN Z 23 65.603 -20.375 -2.291 0.00 0.00 P2
> N
> ATOM 255 HE21 GLN Z 23 65.385 -21.322 -2.509 0.00 0.00 P2
> H
> ATOM 256 HE22 GLN Z 23 66.263 -19.835 -2.801 0.00 0.00 P2
> H
> ATOM 257 N ALA Z 27 71.848 -16.000 0.536 1.00 0.00 P3
> N
> ATOM 258 HT1 ALA Z 27 71.467 -16.828 0.947 0.00 0.00 P3
> H
> ATOM 259 HT2 ALA Z 27 71.113 -15.436 0.160 0.00 0.00 P3
> H
> ATOM 260 HT3 ALA Z 27 72.358 -15.482 1.223 0.00 0.00 P3
> H
> ATOM 261 CA ALA Z 27 72.690 -16.352 -0.465 1.00 0.00 P3
> C
> ATOM 262 HA ALA Z 27 73.417 -16.980 0.038 0.00 0.00 P3
> H
> ATOM 263 CB ALA Z 27 71.790 -17.283 -1.310 0.00 0.00 P3
> C
> ATOM 264 HB1 ALA Z 27 71.261 -17.996 -0.642 0.00 0.00 P3
> H
> ATOM 265 HB2 ALA Z 27 71.022 -16.700 -1.864 0.00 0.00 P3
> H
> ATOM 266 HB3 ALA Z 27 72.383 -17.873 -2.041 0.00 0.00 P3
> H
> ATOM 267 C ALA Z 27 73.478 -15.410 -1.347 1.00 0.00 P3
> C
>
> I do have a warning message saying that "Unusual bond between 26 and 27"...
> What should I do to make sure no residue is missing after run the PSF
> builder.
>
> Meishan
> 

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