VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Jun 06 2007 - 04:37:01 CDT

Hi,

My protein consists of two transmembrane helices connected by a
periplasmic loop. I want to artificially extend one of the helices into
the loop region. One way to do this is to alter the dihedral angles of the
relevant amino acid residues. However, changing the (phi,psi) values of
some of the loop residues to helix specifications (-60,-45) will distort
the topology of the protein downstream of the altered region. Does someone
know of a way to alter dihedral angles of ONLY the specific region of the
protein, while keeping the positions of the rest of the atoms constant ?
Any other suggestions?

Thank you for the help,

----------------------------
Himanshu Khandelia, PhD
MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
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