Re: Remembering resid

From: Branko (
Date: Thu Jun 18 2015 - 08:54:40 CDT


Try to ascribe to each 'piece' of membrane different 'chain' 'name'; for
example 'piece 1' is chain A, 'piece 2' is a chain B etc.


On 6/18/2015 3:42 PM, Kevin C Chan wrote:
> Dear Users,
> I'm struggling with psfgen of a membrane created from duplicating a
> smaller piece of membrane. Obviously there will be duplicated resid
> inside the pdb and psfgen hates them :(
> Then I try to renumber them according to residue choosing ($sel set
> resid [$sel get residue]) but fail as maybe there is a
> user-constructed lipid so VMD is weak at recognising it. It has been a
> nightmare as VMD does not read a topology before load the pdb but only
> a psf. This is weird as I am currently encountering problem when
> making the psf it requires. I thought sending this to the VMD mailing
> list but as it originated from psfgen so I still send it here.
> Can anyone share their experience in making psf for membrane made from
> duplication?
> Thank in advance,
> Kevin
> City University of Hong Kong

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