VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 24 2008 - 23:01:48 CDT

The solution was suggested by Christopher Chang yesterday: turn off
automatic patching.
segment U {
pdb blah.pdb
first none
last none
}

(or, don't just insert your residue into the charmm22 files, which have
default patches defined).

Peter

Rudra Banerjee wrote:
> 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**
>
>