VMD-L Mailing List
From: Cosseddu, Salvatore (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu May 26 2011 - 15:51:49 CDT
- Next message: Salvatore Mario Cosseddu: "Re: tips for an annoying aliasing task?"
- Previous message: Axel Kohlmeyer: "Re: measure fit - wrong alignment"
- In reply to: Edward Lyman: "tips for an annoying aliasing task?"
- Next in thread: Salvatore Mario Cosseddu: "Re: tips for an annoying aliasing task?"
- Reply: Salvatore Mario Cosseddu: "Re: tips for an annoying aliasing task?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Salvatore Mario Cosseddu: "Re: tips for an annoying aliasing task?"
- Previous message: Axel Kohlmeyer: "Re: measure fit - wrong alignment"
- In reply to: Edward Lyman: "tips for an annoying aliasing task?"
- Next in thread: Salvatore Mario Cosseddu: "Re: tips for an annoying aliasing task?"
- Reply: Salvatore Mario Cosseddu: "Re: tips for an annoying aliasing task?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]