VMD-L Mailing List
From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed May 27 2015 - 00:18:58 CDT
As CHARMM-GUI returns membrane of randomly sequential multi-components of
lipids in pdb, I used psfgen to group the same type of lipid. As a result,
the psf and pdb contain non-sequential resID (like
<resid>:1,3,5,...,266,2,4,...,278,...). I guess the files are still
available for production runs, but it is better to have sequential resIDs.
Does anyone have a script for re-numbering these resIDs?
I have noticed a thread on the list (
re-numbering a multi-segment pdb and psf. Unfortunately the codes:
set sel [atomselect top all]
$sel set resid [$sel get residue]
$sel writepdb renumbered.pdb
do not solve my problem as VMD cannot automatically recognize the correct
number of residues, i.e. it may count 3 residue instead of 1 for one single
POPI. I am confused by how VMD counts residues when reading a pdb.
I will appreciate any alternative.
Thanks in advance,
City University of Hong Kong