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<pre wrap="">Dear Blaise,<br><br>To embed a protein into a membrane model, you could try the mdrun program modified by Drs. Tieleman and Smith, available at:<br><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/contributions/index.php">http://www.gromacs.org/contributions/index.php</a><br><br>(Look for <a href="http://www.gromacs.org/contributions/uploaded_contributions/mdrun_make_hole.tar.gz">mdrun_make_hole.tar.gz</a>). A tutorial will be included in share/tutor/make_hole upon installation.<br><br>You will also need to generate accessible molecular surface for your protein with GRASP or MSMS (see tutorial). <br><br>Finally, in your share/top directory, you should include the newest ffgmx_lipids.tar.gz
available at:
<a class="moz-txt-link-freetext" href="http://gromacs.org/topologies/force_fields.php">http://gromacs.org/topologies/force_fields.php</a>
that incorporates the parameters from the lipid.itp.<br><br>Kind regards,<br><br>Martina Be
rtsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611<br><br></pre>
Stud_Psychopharm wrote:<br>
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<pre wrap="">Dear All,<br>I could able to get 128 DPPC (lipid) with water molecules from tielemans <br>site, now I want place my protein (tetramer) into that by removing some <br>number of lipid and water molecules. Is there any program to do that job. <br>Please give soem idea. Many thanks in advance.<br>Regards,<br>Blaise M Costa.<br>------------------------------------------------------------<br>"The more we learn the more we realize how little we know." - <br>R.Buckminster Fuller <br><br>Blaise M.<br>Graduate Student,<br>Department of Psychopharmacology,<br>National Institute of Mental Health And Neuro Sciences (NIMHANS),<br>Bangalore-560029,<br>India. Tel: 91 80 6995112.<br><br><br></pre>
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