VMD-L Mailing List

From: Cosseddu, Salvatore (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu May 26 2011 - 15:51:49 CDT

Try something like this:

proc changename {args} {

for {property oldvalue newvalue} in $args {

set changing [atomselect top "all and $property $oldvalue"]
puts "changing [$changing num] of $property $oldvalue"
$changing set $property $newvalue
$changing delete

}

set all [atomselect top all]
$all writepdp renamed.pdb
$all delete

}

Source this when you load your pdb file as top molecule.

then call

changeneme resname HOH TIP3 <2nd_property> <2nd_oldvalue> <2rd_oldvalue> <3nd_property> <3nd_oldvalue> <3rd_oldvalue>

I haven't tested it

Regards 

--
Salvatore Cosseddu
PhD student 
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
email: S.M.Cosseddu_at_warwick.ac.uk
-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu on behalf of Edward Lyman
Sent: Thu 26/05/2011 16:33
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: tips for an annoying aliasing task?
 
Hi all,
I have a membrane protein system built with Maestro, which I can read
into vmd and write out pdb's for the water, membrane, protein etc. The
naming convention doesn't match charmm though, so I need to alias a
whole lot of atoms. Can anyone offer some effort saving tips for such
a job? (Apart from rebuilding the systme within vmd)
Thx,
Ed