VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Jun 27 2007 - 04:00:50 CDT

This is an incomplete answer as it does not address the bug in your
script.

However, you can also use the following plugin to convert monomers into
multimeric forms. It has worked for me for aquaporins.

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mono2poly/

Hope this helps,

----------------------------
Himanshu Khandelia, PhD
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
University of Southern Denmark (SDU)
Odense M 5230, Denmark

Phone: +4565503510
email: hkhandel_at_memphys.sdu.dk
WWW: www.memphys.sdu.dk/~hkhandel
-----------------------------

On Wed, 27 Jun 2007, Ruchi Sachdeva wrote:

> Hi all,
>
> Im trying to generate a tetramer of aquaporin using the following
> transformation matrix provided in the pdb file.
> **********************
> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
> REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
> REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 96.76000
> REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 96.76000
> REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
> REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 96.76000
> REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000
> REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
> REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000
> REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 96.76000
> REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000
> ******************
>
> i used the following commands in tk console for the purpose
> ****************
> set m1 {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}
> set sel1 [atomselect top "protein and chain A"]
> $sel1 move $m1
> $sel1 writepdb aqp1.pdb
> ****************
>
> Similarly three more pdb files were created with other matrices. Then i put
> all the files in a single pdb file . On viewing the structure in vmd, I
> found only three chains i.e. a trimer rather than a tetramer. Then I noticed
> that structures formed with matrices 2 & 4 had identical coordinates,
> resulting in only three chains.
>
> I followed the same procedure for other pdb's of aquaporins and found same
> error.
>
> Please somebody can tell me what may be the mistake in the procedure?
>
> Any help will be appreciated
>
> Thanks
>