VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jul 15 2007 - 02:02:18 CDT

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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