[gmx-users] Alinging beta sheets

Gaurav Porwal gauravp at che.iitb.ac.in
Fri Jul 23 13:23:23 CEST 2004


>From a secondary structure prediction program, I'm able to get the
regions in the sequence where helices and beta strands are probably
present. As helices are independent structures, the whole region can be
specified as an helix and can be freezed during energy minimization.

The problem arrives in case of beta strands as two strands have to come
close in parallel/antiparallel fashion in order to form a sheet.

Is is possible to construct H bonds in GROMACS such that we can specify
which residues should be forming the bonds, so that two strands can be
forced to come close to form a sheet? In this way, beta sheets can
also be obtained which can later be freezed during energy minimization.

Kindly reply.



It's amazing what a man can accomplish when he's not worried about who
will get the credit.

                           Gaurav Porwal
		    Senior Undergraduate Student
		  Department of Chemical Engineering
                         IIT Bombay, Powai
                          Mumbai - 400076
                          Ph. - 9869277620

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