[gmx-users] I want to know how to make pdb file with 2d structrure file.

Daniela S. Mueller d.s.mueller at rug.nl
Mon Feb 13 00:50:34 CET 2006


to make an (unrealistic) model of a sequence you can use modelling
programs like insight II. there you can model helices or pull your
sequence in space and then write the result to a pdb-file.
this would be your own model determined by yourself and the sequence.
then you can try and fold it using md simulation, but don't expect to
find a native structure easily.


Taeho Kim wrote:
> Hello all.
> I have a secondary structure prediction file of VDAC protein from 
> mitochondrial outer membrane. so I want to make a pdb file with it.
> Which method or programs can be made pdb file?
> thanx.


Daniela S. Mueller

Diplom biologist

-Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732
Email: d.s.mueller at uq.edu.au

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md

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