VMD-L Mailing List

From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Thu Aug 13 2020 - 06:08:42 CDT

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 *
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