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From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Wed Sep 24 2008 - 22:45:49 CDT

dear friends,
I want to repeat one of my unsolved problem. i have a non std. molecule with initial (before generating psf) pdb file is:

 #CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 CD1 MAC A 1 -3.039 1.934 -0.283 1.00 0.00 C
ATOM 2 CG MAC A 1 -3.189 0.892 0.625 1.00 0.00 C
ATOM 3 CD2 MAC A 1 -2.112 0.042 0.894 1.00 0.00 C
ATOM 4 CE2 MAC A 1 -0.879 0.204 0.276 1.00 0.00 C
ATOM 5 CZ MAC A 1 -0.733 1.261 -0.643 1.00 0.00 C
ATOM 6 CE1 MAC A 1 -1.812 2.120 -0.917 1.00 0.00 C
ATOM 8 C3 MAC A 1 1.315 -0..482 -0.029 1.00 0.00 C
ATOM 9 C2 MAC A 1 1.562 0.544 -0.962 1.00 0.00 C
ATOM 10 C1 MAC A 1 0.512 1.419 -1.262 1.00 0.00 C
ATOM 11 C7 MAC A 1 2.353 -1.354 0.273 1.00 0.00 C
ATOM 12 C6 MAC A 1 3.613 -1.234 -0.321 1.00 0.00 C
ATOM 13 C5 MAC A 1 3.854 -0.212 -1.232 1.00 0.00 C
ATOM 14 C4 MAC A 1 2.827 0.670 -1.563 1.00 0.00 C
ATOM 24 C8 MAC A 1 5.628 -2.116 -0.419 1.00 0.00 C
ATOM 25 CA MAC A 1 -5.107 1.352 1.005 1.00 0.00 C
ATOM 26 CB MAC A 1 -4.392 -0.073 1.897 1.00 0..00 C
ATOM 36 C9 MAC A 1 4.407 -3.273 0.925 1..00 0.00 C
ATOM 7 N MAC A 1 0.123 -0.642 0.571 1.00 0.00 N
ATOM 15 N1 MAC A 1 4.671 -2.189 0.006 1.00 0.00 N
ATOM 16 N2 MAC A 1 -4.299 0.713 1.207 1.00 0.00 N
ATOM 17 HD1 MAC A 1 -3.879 2.612 -0.492 1.00 0.00 H
ATOM 18 HD2 MAC A 1 -2.248 -0.784 1.607 1.00 0.00 H
ATOM 19 HE1 MAC A 1 -1.685 2.949 -1.629 1.00 0.00 H
ATOM 20 H1 MAC A 1 0.669 2.239 -1.978 1.00 0.00 H
ATOM 21 H7 MAC A 1 2.175 -2.167 0.992 1.00 0.00 H
ATOM 22 H5 MAC A 1 4.846 -0.106 -1.696 1.00 0.00 H
ATOM 23 H4 MAC A 1 3.013 1.474 -2.290 1.00 0.00 H
ATOM 27 H81 MAC A 1 6.081 -1.136 -0.148 1.00 0.00 H
ATOM 28 H82 MAC A 1 5.550 -2.185 -1.527 1.00 0.00 H
ATOM 29 H83 MAC A 1 6.270 -2.939 -0.032 1.00 0.00 H
ATOM 30 HA2 MAC A 1 -4.830 2.397 1.270 1.00 0.00 H
ATOM 31 HA1 MAC A 1 -5.986 1..045 1.614 1.00 0.00 H
ATOM 32 HA3 MAC A 1 -5.354 1.307 -0.080 1.00 0.00 H
ATOM 33 HB2 MAC A 1 -5.425 -0.085 2.310 1.00 0.00 H
ATOM 34 HB3 MAC A 1 -4.187 -1.041 1.386 1.00 0.00 H
ATOM 35 HB1 MAC A 1 -3.663 0.071 2.725 1.00 0.00 H
ATOM 37 H93 MAC A 1 3.586 -3.909 0.524 1.00 0.00 H
ATOM 38 H92 MAC A 1 5.323 -3.895 1.040 1.00 0.00 H
ATOM 39 H91 MAC A 1 4.096 -2.858 1.910 1.00 0.00 H
END

and for this molecule, i have generated my topology file(inserted to charmm22 protein topology file)is:
!MY RESIDUE

RESI MAC 0.00
GROUP
ATOM N2 NH2 -0.47 !
ATOM HA1 HB 0.31 !
ATOM CA CA 0.07 !
ATOM HA2 HB 0.09 !
ATOM HA3 HB 0.00 !
GROUP !
ATOM CB CA -0.18 !
ATOM HB1 HB 0.09 !
ATOM HB2 HB 0..09 !
ATOM HB3 HB 0.00 !
GROUP !
ATOM CD1 CA -0.115 !
ATOM HD1 HP 0.115 !
GROUP !
ATOM CE1 CA -0.115 !
ATOM HE1 HP 0.115 ! HE1 H1 H4
GROUP ! | | |
ATOM CZ CA 0.00 ! HA2 HD1 CE1 C1 C4 H5 H83
GROUP ! | \ // \ / \\ / \\ / |
ATOM CG CA 0.00 ! HA1-CA CD1 CZ C2 C5 --C8-H82
GROUP ! | | || | | \
ATOM CD2 CA -0.115 ! HA3 N2-- CG CE2 C3 C6-N1 H81
ATOM HD2 HP 0.115 ! | \\ / \ // \ // |
GROUP ! HB1-CB-HB3 CD2 N C7 C9-H93
ATOM CE2 CA 0.47 ! | | / / \
ATOM N NR3 -0.47 ! HB2 HD2 H7 H91 H92
GROUP !
ATOM C1 CA -0.115 !
ATOM H1 HP 0.115 !
GROUP !
ATOM C2 CA 0.00 !
ATOM C3 CA 0.00 !
GROUP !
ATOM C4 CA -0.115 !
ATOM H4 HP 0.115 !
GROUP !
ATOM C5 CA -0.115 !
ATOM H5 HP 0.115 !
GROUP !
ATOM C7 CA -0.115 !
ATOM H7 HP 0.115 !
GROUP !
ATOM C6 CA 0.07 !
ATOM N1 NH2 -0.047 !
ATOM C8 CA 0.08 !
ATOM C9 CA 0.08 !
ATOM H81 HB 0.04 !
ATOM H82 HB 0.04 !
ATOM H83 HB 0.04 !
ATOM H91 HB 0.04 !
ATOM H92 HB 0.04 !
ATOM H93 HB 0.04 !
BOND CG CD1 CE1 CZ CZ C1 C2 C3 CE2 CD2 CE2 N C2 C4 C5 C6 N2 CG N1 C6
BOND N2 CA CA HA1 CA HA2 CA HA3 N2 CB CB HB1 CB HB2 CB HB3
BOND CD1 HD1 CE1 HE1 C1 H1 C4 H4 C5 H5 C7 H7 CD2 HD2 C7 C3
BOND N1 C8 N1 C9 C9 H91 C9 H92 C9 H93 C8 H81 C8 H82 C8 H83
DOUBLE CD1 CE1 CG CD2 CZ CE2 C1 C2 C3 N C4 C5 C6 C7

but when i am trying to generate psf file using vmd using the .pgn file (cku.pgn)

package require psfgen
topology my-top.inp
#pdbalias residue HIS HSE
#pdbalias atom ILE CD1 CD
segment U {pdb ao_tst.pdb}
coordpdb ao_tst.pdb U
guesscoord
writepdb aoq.pdb
writepsf aoq.psf

using the command:
$vmd -dispdev text -e cku.pgn

then i am getting a few extra atom(6 actually) in (0 0 0) position with occupency -1. here is that (part of) generated pdb file:

REMARK original generated coordinate pdb file
ATOM 1 C MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 2 OT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O
ATOM 3 OT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O
ATOM 4 N MAC 0 0.123 -0.642 0.571 1.00 0.00 U N
ATOM 5 HT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 6 HT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 7 HT3 MAC 0 0.000 0..000 0.000 -1.00 0.00 U H
ATOM 8 CA MAC 0 -5.107 1.352 1.005 1.00 0.00 U C
ATOM 9 HA MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 10 N2 MAC 0 -4.299 0.713 1.207 1.00 0.00 U N
...
...

those occupency with -1 is troublesome and i need to remove them. any idea where i am going wrong?looking fwd for your suggestions.
**NB. plz ignore if there is any double decimal...its somehow due to formatting** 

-- 
Rudra
JRF; SNBNCBS
http://www.bose.res.in/~rudra
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