VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Jul 15 2007 - 17:36:04 CDT

Hi Irene,
you may also want to avoid having an atom name in the patch entry that
is simultaneously being deleted (eg, 1HO1/2HO3/2O3 in the GB13 patch).
This is likely to confuse psfgen, as it is being told to delete the
atoms and then add them again. If you're trying to just modify the
properties there's no need to delete them, and vice versa.

Peter

JC Gumbart wrote:
> 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
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