Re: psf gen

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Sep 07 2008 - 08:03:40 CDT

Hi Rudra,
where are at least two problems here... one is that your pdb file
appears corrupt (several of the coordinates have multiple decimal
points). The second is that according to the psfgen error, you don't
have a topology entry for this residue. You can name the residue pretty
much anything you want that isn't already taken in the topology files
you're using; you then need to make a topology file entry for it and you
should be fine. Some of the associated procedures are described in the
Topology file tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/#topology) and Parameterizing
a novel residue tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/).

Peter

Rudra Banerjee wrote:
> dear friends,
> i need to generate psf file of cridine orange.
> i have managed to get the pdb and managed to create the pdb without H atoms as told in tutorial.
> but whem i am trying to create psf file, its showing error.
> py pdb file is :
>
> ATOM 1 C X 1 -3.039 1.934 -0..283 0.00 0.00 C
> ATOM 2 C X 1 -3.189 0.892 0.625 0.00 0.00 C
> ATOM 3 C X 1 -2.112 0.042 0.894 0.00 0.00 C
> ATOM 4 C X 1 -0.879 0.204 0.276 0.00 0.00 C
> ATOM 5 C X 1 -0.733 1.261 -0.643 0.00 0.00 C
> ATOM 6 C X 1 -1.812 2.120 -0.917 0.00 0.00 C
> ATOM 7 N X 1 0.123 -0.642 0.571 0.00 0.00 N
> ATOM 8 C X 1 1.315 -0.482 -0.029 0.00 0.00 C
> ATOM 9 C X 1 1.562 0.544 -0.962 0.00 0.00 C
> ATOM 10 C X 1 0.512 1.419 -1.262 0.00 0.00 C
> ATOM 11 C X 1 2.353 -1.354 0.273 0.00 0.00 C
> ATOM 12 C X 1 3.613 -1.234 -0.321 0.00 0.00 C
> ATOM 13 C X 1 3.854 -0.212 -1.232 0.00 0.00 C
> ATOM 14 C X 1 2.827 0.670 -1.563 0.00 0.00 C
> ATOM 15 N X 1 4.671 -2.189 0.006 0.00 0.00 N
> ATOM 16 N X 1 -4...299 0.713 1.207 0.00 0.00 N
> ATOM 17 H X 1 -3.879 2.612 -0.492 0.00 0.00 H
> ATOM 18 H X 1 -2.248 -0.784 1.607 0.00 0.00 H
> ATOM 19 H X 1 -1.685 2.949 -1.629 0.00 0.00 H
> ATOM 20 H X 1 0.669 2.239 -1.978 0.00 0.00 H
> ATOM 21 H X 1 2.175 -2.167 0.992 0.00 0.00 H
> ATOM 22 H X 1 4.846 -0.106 -1.696 0.00 0.00 H
> ATOM 23 H X 1 3.013 1.474 -2.290 0.00 0.00 H
> ATOM 24 C X 1 5.628 -2.116 -0.419 0.00 0.00 C
> ATOM 25 C X 1 -5.107 1.352 1.005 0.00 0.00 C
> ATOM 26 C X 1 -4.392 -0.073 1.897 0.00 0.00 C
> ATOM 27 H X 1 6.081 -1...136 -0.148 0.00 0.00 H
> ATOM 28 H X 1 5.550 -2.185 -1.527 0.00 0.00 H
> ATOM 29 H X 1 6.270 -2.939 -0.032 0.00 0.00 H
> ATOM 30 H X 1 -4.830 2.397 1.270 0.00 0.00 H
> ATOM 31 H X 1 -5.986 1.045 1.614 0.00 0.00 H
> ATOM 32 H X 1 -5.354 1.307 -0.080 0.00 0.00 H
> ATOM 33 H X 1 -5.425 -0.085 2.310 0.00 0.00 H
> ATOM 34 H X 1 -4.187 -1.041 1.386 0.00 0.00 H
> ATOM 35 H X 1 -3.663 0.071 2.725 0.00 0.00 H
> ATOM 36 C X 1 4.407 -3.273 0.925 0.00 0..00 C
> ATOM 37 H X 1 3.586 -3.909 0.524 0..00 0.00 H
> ATOM 38 H X 1 5.323 -3.895 1.040 0.00 0.00 H
> ATOM 39 H X 1 4.096 -2.858 1.910 0.00 0.00 H
> END
>
> and pgn file is
>
> package require psfgen
> topology top_all22_prot.inp
> #pdbalias atom ILE CD1 CD
> segment U {pdb ao.pdb}
> coordpdb ao.pdb U
> guesscoord
> writepdb aoq.pdb
> writepsf aoq.psf
>
> the error is (obviously) unknown residue as prompted:
> $vmd -dispdev text -e cku.pgn
> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Free system memory: 2607MB (86%)
> 1.4.5
> reading topology file top_all22_prot.inp
>
>
>>>>>>>>> CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>
> December 2003
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<
> All comments to ADM jr. via the CHARMM web site: www.charmm.org
> parameter set discussion forum
>
> Created by CHARMM version 22 1
> building segment U
> reading residues from pdb file ao.pdb
> unknown residue type
> extracted 1 residues from pdb file
> Info: generating structure...
> unknown residue type
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
> vmd >
>
>
> can anybody suggest me how can i get around with this porblem and how how to choose residue name?
>
>

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