VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Sun Jul 15 2007 - 18:37:46 CDT

Thanks so much for the suggestion, but the result is exactly the same as before.

Irene

----------------------------------------
> From: gumbart_at_ks.uiuc.edu
> To: einew_at_hotmail.com; vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: atoms deleted in patch try to come back
> Date: Sun, 15 Jul 2007 02:02:18 -0500
>
> If I had to guess, I'd say to put the coordpdb command after the patch
> commands. :)
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Irene Newhouse
> Sent: Sunday, July 15, 2007 1:02 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: atoms deleted in patch try to come back
>
>
> I've written a patch which half works. The atoms that are supposed to be
> deleted are still there, but they're placed at the origin & assigned
> occupancies of -1.00 in the pdb file. They only appear in the atom list in
> the psf file, not in the bonds, angles or dihedrals section. I could edit
> them out & ignore the problem, but I'd really like to know what embarrassing
> mistake I'm making this time. I can't seem to be able to send a gz tarball
> of the associated files, so I'm going to append
>
> 1. the psf command file:
>
> package require psfgen
> topology top_kitsink.inp
> segment L {pdb LSTa.pdb}
> coordpdb LSTa.pdb L
> patch SG23 L:1 L:2
> patch GB13 L:2 L:3
> patch BETA L:4
> patch GB13 L:3 L:4
> patch BETA L:5
> patch GB14 L:4 L:5
> guesscoord
> writepdb lstaf.pdb
> writepsf lstaf.psf
> exit
>
> 2. the pdb file:
>
> REMARK 888
> REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
> MODEL 1
> HETATM 1 C1 SIA 1 -3.420 -0.503 -0.012 1.00 0.00
> C
> HETATM 2 C2 SIA 1 -2.522 0.686 0.285 1.00 0.00
> C
> HETATM 3 C3 SIA 1 -2.291 0.867 1.814 1.00 0.00
> C
> HETATM 4 C4 SIA 1 -1.402 -0.238 2.389 1.00 0.00
> C
> HETATM 5 C5 SIA 1 -0.114 -0.344 1.558 1.00 0.00
> C
> HETATM 6 C6 SIA 1 -0.482 -0.537 0.065 1.00 0.00
> C
> HETATM 7 C7 SIA 1 0.785 -0.628 -0.821 1.00 0.00
> C
> HETATM 8 C8 SIA 1 0.422 -0.885 -2.303 1.00 0.00
> C
> HETATM 9 C9 SIA 1 1.683 -1.005 -3.171 1.00 0.00
> C
> HETATM 10 C10 SIA 1 1.942 -1.315 2.497 1.00 0.00
> C
> HETATM 11 C11 SIA 1 2.732 -2.511 2.930 1.00 0.00
> C
> HETATM 12 N5 SIA 1 0.673 -1.476 2.031 1.00 0.00
> N
> HETATM 13 O1A SIA 1 -3.380 -1.060 -1.252 1.00 0.00
> O
> HETATM 14 O1B SIA 1 -4.270 -0.876 0.828 1.00 0.00
> O
> HETATM 15 O2 SIA 1 -3.231 1.820 -0.206 1.00 0.00
> O
> HETATM 16 O4 SIA 1 -1.094 0.074 3.723 1.00 0.00
> O
> HETATM 17 O6 SIA 1 -1.280 0.541 -0.407 1.00 0.00
> O
> HETATM 18 O7 SIA 1 1.507 0.575 -0.713 1.00 0.00
> O
> HETATM 19 O8 SIA 1 -0.322 -2.074 -2.403 1.00 0.00
> O
> HETATM 20 O9 SIA 1 1.322 -1.226 -4.507 1.00 0.00
> O
> HETATM 21 O10 SIA 1 2.516 -0.090 2.566 1.00 0.00
> O
> HETATM 22 C1 AGA 2 -2.371 5.480 -0.430 1.00 0.00
> C
> HETATM 23 C2 AGA 2 -3.138 4.222 0.022 1.00 0.00
> C
> HETATM 24 C3 AGA 2 -2.411 2.953 -0.469 1.00 0.00
> C
> HETATM 25 C4 AGA 2 -2.142 3.061 -1.983 1.00 0.00
> C
> HETATM 26 C5 AGA 2 -1.437 4.405 -2.274 1.00 0.00
> C
> HETATM 27 O5 AGA 2 -2.249 5.482 -1.843 1.00 0.00
> O
> HETATM 28 O1 AGA 2 -3.106 6.615 -0.001 1.00 0.00
> O
> HETATM 29 O2 AGA 2 -3.225 4.213 1.424 1.00 0.00
> O
> HETATM 30 O4 AGA 2 -3.361 2.985 -2.682 1.00 0.00
> O
> HETATM 31 C6 AGA 2 -1.138 4.568 -3.768 1.00 0.00
> C
> HETATM 32 O6 AGA 2 -0.432 5.760 -3.977 1.00 0.00
> O
> HETATM 33 C1 NAG 3 -2.656 10.067 -1.494 1.00 0.00
> C
> HETATM 34 C2 NAG 3 -3.246 8.653 -1.345 1.00 0.00
> C
> HETATM 35 C3 NAG 3 -2.505 7.896 -0.223 1.00 0.00
> C
> HETATM 36 C4 NAG 3 -0.963 7.973 -0.410 1.00 0.00
> C
> HETATM 37 C5 NAG 3 -0.510 9.424 -0.734 1.00 0.00
> C
> HETATM 38 O5 NAG 3 -1.269 9.998 -1.790 1.00 0.00
> O
> HETATM 39 O1 NAG 3 -3.327 10.717 -2.560 1.00 0.00
> O
> HETATM 40 N2 NAG 3 -3.156 7.943 -2.615 1.00 0.00
> N
> HETATM 41 O4 NAG 3 -0.319 7.516 0.753 1.00 0.00
> O
> HETATM 42 C6 NAG 3 -0.411 10.353 0.497 1.00 0.00
> C
> HETATM 43 C7 NAG 3 -4.268 7.443 -3.225 1.00 0.00
> C
> HETATM 44 C8 NAG 3 -4.171 6.806 -4.579 1.00 0.00
> C
> HETATM 45 O7 NAG 3 -5.477 7.473 -2.615 1.00 0.00
> O
> HETATM 46 O6 NAG 3 -0.151 11.665 0.080 1.00 0.00
> O
> HETATM 47 C1 AGA 4 -4.217 14.302 -3.220 1.00 0.00
> C
> HETATM 48 C2 AGA 4 -4.421 12.785 -3.093 1.00 0.00
> C
> HETATM 49 C3 AGA 4 -3.152 12.128 -2.527 1.00 0.00
> C
> HETATM 50 C4 AGA 4 -1.934 12.543 -3.377 1.00 0.00
> C
> HETATM 51 C5 AGA 4 -1.889 14.078 -3.580 1.00 0.00
> C
> HETATM 52 O5 AGA 4 -3.119 14.592 -4.073 1.00 0.00
> O
> HETATM 53 O1 AGA 4 -5.392 14.860 -3.779 1.00 0.00
> O
> HETATM 54 O2 AGA 4 -5.509 12.535 -2.240 1.00 0.00
> O
> HETATM 55 C6 AGA 4 -1.373 14.842 -2.343 1.00 0.00
> C
> HETATM 56 O4 AGA 4 -2.000 11.903 -4.627 1.00 0.00
> O
> HETATM 57 O6 AGA 4 -1.437 16.222 -2.579 1.00 0.00
> O
> HETATM 58 O5 AGL 5 -6.680 18.151 -2.805 1.00 0.00
> O
> HETATM 59 C5 AGL 5 -6.618 16.735 -2.849 1.00 0.00
> C
> HETATM 60 C4 AGL 5 -5.397 16.279 -3.683 1.00 0.00
> C
> HETATM 61 C3 AGL 5 -5.503 16.867 -5.100 1.00 0.00
> C
> HETATM 62 C2 AGL 5 -5.746 18.387 -5.032 1.00 0.00
> C
> HETATM 63 C1 AGL 5 -6.932 18.682 -4.093 1.00 0.00
> C
> HETATM 64 C6 AGL 5 -6.528 16.208 -1.412 1.00 0.00
> C
> HETATM 65 O3 AGL 5 -4.315 16.604 -5.801 1.00 0.00
> O
> HETATM 66 O2 AGL 5 -6.033 18.884 -6.314 1.00 0.00
> O
> HETATM 67 O1 AGL 5 -7.095 20.070 -3.968 1.00 0.00
> O
> HETATM 68 O6 AGL 5 -7.637 16.649 -0.679 1.00 0.00
> O
> END
>
> and 3: the patch. That's not enough to try to reproduce my problem. I'll be
> happy to send you my entire modified topology file if you ask.
>
> PRES GB13 0.16 ! C1 of beta pyranose to C3
> GROU ! modelled on DISU ein 7/07
> ATOM 1C2 CTS 0.14
> ATOM 1C1 CTS 0.20
> ATOM 1O1 OHS -0.66
> ATOM 1HO1 HOS 0.43
> GROU
> ATOM 2HO3 HOS 0.43
> ATOM 2O3 OHS -0.66
> ATOM 2C3 CTS 0.14
> ATOM 2C2 CTS 0.14
>
> DELETE ATOM 1HO1
> DELETE ATOM 2HO3
> DELETE ATOM 2O3
>
> BOND 1O1 2C3
>
> AUTO ANGLES DIHE
> !IC 1C2 1C1 1O1 2C3 0.00 0.00 -179.4 0.00 0.00
> !IC 1C1 1O1 2C3 2C2 0.00 0.00 89.58 0.00 0.00
> !IC 1O1 2C3 2C2 2C1 0.00 0.00 176.21 0.00 0.00
>
> It doesn't matter whether I use the ICs or the AUTO - it acts just the same.
>
> Thanks!
>
> Irene Newhouse
> _________________________________________________________________
> See what you're getting into.before you go there.
> http://newlivehotmail.com
>

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