VMD-L Mailing List

From: Baoqiang Cao (caobg_at_email.uc.edu)
Date: Tue Sep 27 2005 - 21:10:07 CDT

Dear All,

It is sure that there are 2 missing segments in the original pdb file,
for example, 1-10 and 100-130 are missing. I followed one of the online
documents to write out pdb coordinates and the corresponding psf file
for further use. What I did is:

######################
mol load pdb original.pdb
set protein [atomselect top protein]
set chains [lsort -unique [$protein get pfrag]]
foreach chain $chains {
  set sel [atomselect top "pfrag $chain"]
  $sel writepdb myfile_seg${chain}.pdb
}
package require psfgen
topology top_all27_prot_lipid.inp
foreach chain $chains {
        segment myseg${chain} {
                first NONE
                last NONE
                pdb myfile_seg${chain}.pdb
                }
}
foreach chain $chains {
        coordpdb myfile_seg${chain}.pdb myseg${chain}
}
writepsf protein.psf
#######################

It is a one chain protein in orignal.pdb with 2 missing segments as
described above. But, it got 4 chains, and, couldn't write any thing in
protein.psf and protein.pdb. Any body show me where went wrong? Thanks!

Best,
 Baoqiang Cao