VMD-L Mailing List
From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Thu Aug 13 2020 - 06:08:42 CDT
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Hi.
I am trying to simulate organic nanotube in lipid bilayer. At this place as
the nanotube is having 650 atoms, I couldn't find a way to generate PSF
files.
I have two files roll.pdb and membrane.pdb. (Both the pdb files don't have
chain id)
My commands are
>Main< (Roll_vmd) 12 % *set popc [atomselect top all]*
atomselect0
>Main< (Roll_vmd) 14 % *set roll [mol new trial.pdb]*
1
>Main< (Roll_vmd) 17 % *$popc moveby [vecinvert [measure center $popc
weight mass]]*
>Main< (Roll_vmd) 18 % *$popc writepdb popc_temp.pdb*
BY this step, I have the pdb file for popc and water molecules with chain
ID X for all the molecules (popc and water)
>Main< (Roll_vmd) 19 % *set vest [atomselect $roll "resname MOL"]*
atomselect1
>> How do I know what atoms are selected in this "atomselect1"
>Main< (Roll_vmd) 21 % *$roll moveby [vecinvert [measure center $vest
weight mass]]*
invalid command name "2"
I have tried various options and still I couldn't find the way to align the
roll to the center of the lipid and remove the bad lipids.
-- *Regards,* *Rahul * Create your own email signature <https://chrome.google.com/webstore/detail/free-email-signature-gene/adabkammndnejioekmmdhgdnlfenpkci>
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