Box size is in the last line of the coordinate file, both .gro and .pdb will have the box size / dimensions there.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Mohana lakshmi Sent: Sunday, 20 March 2011 3:50 AM To: gromacs users Subject: [gmx-users] Fw: g_membed tool Dear all.. I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane strucuture file but i don t know how and where to mention the size? Whether any tutorial is available for transmembrane protein using g_membed tool? Thank you Mohanalakshmi N.
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