VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 02 2010 - 12:51:24 CDT

Hi,
  "MOLID" should have been a numeric value, e.g. the output of the
command "molinfo top" for example:
  autopsf -mol 0
or
  autopsf -mol [molinfo top]

This is the kind of thing I think you would understand better if you
worked your way through the various VMD tutorials before going into this...

Cheers,
  John

On Wed, Jun 02, 2010 at 11:44:33AM -0500, vani panguluri wrote:
> hi,
> i am following those tutorials only but i am unable to get the
> result .the commands which you people specified in the autopsf gen
> tutorial only i am using. can you please explain how to work on those
> commands clearly i am attaching a file that contains the commands which i
> am using and what are the errors i am geeting.
> Thanks & Regards,
> Vani

> (VMD) 1 % autopsf -mol MOLID
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: MOLID
> pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
> expected integer but got "MOLID"Not valid molecule id MOLID in atomselect's 'molId'
> >Main< (VMD) 2 % -protein
> invalid command name "-protein"
> >Main< (VMD) 3 % autopsf -protein
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
> Need to have at least one atom in your selection!
> >Main< (VMD) 4 % autopsf -nucleic popc128a.pdb
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: false osel: protein or nucleic nfrag: true
> Need to have at least one atom in your selection!
> >Main< (VMD) 5 % autopsf -nucleic atom
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: false osel: protein or nucleic nfrag: true
> Need to have at least one atom in your selection!
> >Main< (VMD) 6 % autopsf -protein n2
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
> Need to have at least one atom in your selection!
> >Main< (VMD) 7 % autopsf -noguess
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
> Reading PDB CONECT records...
> Warning: I couldn't find the original pdb to assign connectivity
> Using autogenerated connectivity only
> ERROR: psf checking did not work correctly.
> There may be something wrong with the input structure.
> 2
> >Main< (VMD) 8 % autopsf -noguess popc128a.pdb
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
> Reading PDB CONECT records...
> Warning: I couldn't find the original pdb to assign connectivity
> Using autogenerated connectivity only
> ERROR: psf checking did not work correctly.
> There may be something wrong with the input structure.
> 2
> >Main< (VMD) 9 % autopsf -noguess C:\Users\VANITEJA\Documents\Downloads
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
> Reading PDB CONECT records...
> Warning: I couldn't find the original pdb to assign connectivity
> Using autogenerated connectivity only
> ERROR: psf checking did not work correctly.
> There may be something wrong with the input structure.
> 2
> >Main< (VMD) 10 % autopsf -noguess C:\Users\VANITEJA\Documents\Downloads\popc128a.pdb
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
> Reading PDB CONECT records...
> Warning: I couldn't find the original pdb to assign connectivity
> Using autogenerated connectivity only
> ERROR: psf checking did not work correctly.
> There may be something wrong with the input structure.
> 2
> >Main< (VMD) 11 % autopsf -noguess C:\Users\VANITEJA\Documents\Downloads\popc128a.pdb
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: false ofrag: false allfrag: true osel: protein or nucleic nfrag: false
> Reading PDB CONECT records...
> Warning: I couldn't find the original pdb to assign connectivity
> Using autogenerated connectivity only
> ERROR: psf checking did not work correctly.
> There may be something wrong with the input structure.
> 2
> >Main< (VMD) 12 % connect
> invalid command name "connect"
> invalid command name "connect"
> >Main< (VMD) 13 % -molid $molid
> can't read "molid": no such variable
> >Main< (VMD) 14 % $molid
> can't read "molid": no such variable
> >Main< (VMD) 15 % pbcwrap $molid
> can't read "molid": no such variable
> >Main< (VMD) 16 % pbcwrap -molid $molid
> can't read "molid": no such variable
> >Main< (VMD) 17 % pbcwrap $molid
> can't read "molid": no such variable
> >Main< (VMD) 18 % autopsf -protein N
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
> Need to have at least one atom in your selection!
> >Main< (VMD) 19 % autopsf -protein Ni
> Welcome to AUTOPSF!
> The automatic structure builder.
> WORKING ON: top
> pfrag: true ofrag: false allfrag: false osel: protein or nucleic nfrag: false
> Need to have at least one atom in your selection!
> >Main< (VMD) 20 % 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078