[gmx-users] RE: Insertion of protein in lipid bilayer

[Graham Smith]

>From naga raju nagaraju_cy at yahoo.co.in
>Tue Jul 26 12:48:31 CEST 2005

>1) To genarate *.tpr file which pdb file to be taken,
>initial structure or generated by make_hole.pl
>program.

generated by make_hole.pl

>2)After doing above process, i couldn't see the hole
>in the molecule. Could you tell me the correct
>procedure.

Run with debugsurf = yes in the mdp file, and view the pdb file that it
will write. You will be able to check that some atoms do really have
"hole-making" forces on them.

If nothing happenes, increase the force constant? (you might need
restraints to keep the leaflets together).

Graham

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Dr Graham R. Smith
Biosystems Informatics Institute
2nd Floor, Bioscience Centre
International Centre for Life
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Newcastle upon Tyne
NE1 4EP

Phone: +44 (0)191 211 2606
Mobile: +44 (0)7812 455 010
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e-mail: graham.smith at biiuk.com
http://www.biiuk.com

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