Re: vmd-l: CMAP problem

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 03 2006 - 14:39:37 CST

Hi,
  I now see what your problem is. This is specifically the psfgen plugin
that you're having trouble with, not simply loading PSF files with the CMAP
feature into VMD. The psfgen plugin doesn't yet read these CMAP files.
I'll have to defer to Jim as to when psfgen may be updated to support
CMAP in psfgen, as there's much more to this than merely reading the CMAP
records from the PSF files in the case of psfgen/NAMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 03, 2006 at 01:28:22PM -0700, Morad Alawneh wrote:
> *Thanks for your replying.
>
> I am using both vmd 1.8.4b6 and namd 2.6b1.
>
> when executing my script, I got this message
> ERROR! FAILED TO RECOGNIZE CMAP
>
>
> This is my script :
>
> # Delete any previous molecules
> mol delete all
> resetpsf
>
> # Make psfgen package available to be called by vmd
> package require psfgen
>
> # Use the specified topology file.
> topology top_all27_prot_lipid.inp
> #topology 22/top_all22_lipid.inp
>
> # Build one segment of lipid.
> segment LIP {
> first NONE
> last NONE
> residue 1 DMPC }
>
> # Give coordinates for one atom.
> coord Lip 1 N {0.0 0.0 0.0}
>
> # Guess the positions of missing atoms, as long as
> # all the heavy atoms are present.
> guesscoord
>
> # Write out the psf file
> writepsf charmm dmpc.psf
>
> # Write out the pdb file
> writepdb dmpc.pdb
>
>
>
>
> Thanks*
>
>
>
> John Stone wrote:
> >Hi,
> > The latest PSF reader plugin for VMD already reads PSF files
> >that contain the CMAP option. If you have trouble using these files
> >with either an update VMD 1.8.3, or with the latest test versions of
> >VMD 1.8.4 please let me know. Jim can answer in regards to the NAMD side
> >of things.
> >
> > John
> >
> >On Tue, Jan 03, 2006 at 12:45:41PM -0700, Morad Alawneh wrote:
> >
> >>When is CMAP algorithm be implemented in both VMD and NAMD, in order to
> >>be able to use the new charmm parameter files, 27?
> >>
> >>Thanks
> >>--
> >>
> >>
> >>
> >>/*Morad Alawneh*/
> >>
> >>*Department of Chemistry and Biochemistry*
> >>
> >>*C100 BNSN, BYU*
> >>
> >>*Provo, UT 84602*
> >>
> >>
> >
> >
>
> --
>
>
>
> /*Morad Alawneh*/
>
> *Department of Chemistry and Biochemistry*
>
> *C100 BNSN, BYU*
>
> *Provo, UT 84602*
>

-- 
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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:29 CST