VMD-L Mailing List

From: jouko_at_berkeley.edu
Date: Tue Jan 06 2009 - 16:31:46 CST

I am trying to convert a dcd file that is larger than 7 GB to individual
pdb files. When I run the script I normally use to convert dcd files to
pdb files vmd aborts. The script is pasted below.

mol load psf ubq_solution_wb.psf dcd ubq_wb.12ns.dcd
set nf [molinfo top get numframes]
for {set i 0} {$i<$nf} {incr i} {[atomselect top all frame $i] writepdb
/home/jouko/1ubq_phosphate5/0-3_ns/ubq_$i.pdb}

I was thinking that the dcd file might be too large to be read by vmd, so
I thought I could split it up using sed. However when I do that vmd is
not able to read the split up dcd files, except for the first one. Any
help would be appreciated.

Thanks,

Jouko