VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 29 2006 - 11:55:49 CDT

On 8/29/06, wang <c00jsw00_at_nchc.org.tw> wrote:
> Dear Dimka ,
> Thanks for your help . But the script still didn't work . @@
> Could you know how to using C or fortran to read dcd file ?

please check the availability of disk space. the pdb files
will consume multiple times the space than the .dcd trajectory
(and i'm curious to learn what you need those many .pdb
file for in the first place).

you can actually use the molfile plugins bundled with vmd
to read your dcd file (and write pdb) if needed. see:
http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/
for more details.

the script improvements suggested by people here, have no
obvious flaw, so there must be something else going wrong.
my guess is, that if you program the converter yourself you'll
also find it not to work.

cheers,
   axel.

> thx
> wang
>
>
>
>
>
>
>
>
>
> dimka 提到:
>
> > also since you redefine the variable "all" with each iteration you may
> > run out of memory before your script completes, a better script would
> > be...
> >
> > mol load psf all.psf dcd 1.dcd
> > set nf [molinfo top get numframes]
> > set all [atomselect top all]
> > for {set i 0 } {$i < $nf} {incr i} {
> > $all frame $i
> > $all writepdb $i.pdb
> > }
> >
> >
> > On 8/29/06, dimka <newyorkdimka_at_gmail.com> wrote:
> >
> >> ran out of quota/disk space? file is greater than 2gb and operating
> >> system cannot support >2gb files...
> >>
> >> On 8/29/06, wang <c00jsw00_at_nchc.org.tw> wrote:
> >> > Dear all ,
> >> > I used VMD software to transform dcd file (from NAMD) into pdb
> >> format file .
> >> > There are 30000 frames in dcd file . But I only tranfromed 4500 pdb
> >> files .
> >> > Could you tell me how to fix the problem ?
> >> > thx
> >> > wang ^^
> >> >
> >> >
> >> > my script
> >> > _____________________________________________________
> >> > mol load psf all.psf dcd 1.dcd
> >> > set nf [molinfo top get numframes]
> >> > for {set i 0 } {$i < $nf} {incr i}
> >> > {
> >> > set all [atomselect top all frame $i ]
> >> > $all writepdb $i.pdb
> >> > }
> >> >
> >> >
> >>
> >
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.