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<DIV><FONT face=Arial size=2>Hi all:<BR>I have a basic question here. I want to
simulate a infinite alpha-helix protein, say alanine represented using a unit
cell containning 11 residues.<BR>Now I want to simulate it in GROMACS but
don't know how to generate TOP for the structure, i.e. the connectivity
between the 1st residue and image of 11th residue. Conventional TOP
generation process using pdb2gmx will terminated them rather than fit my
need.<BR>Could anyone here give me a hand? Thanks.<BR>Best,<BR>ZP </FONT></DIV>
<DIV><FONT face=Arial size=2>-- <BR>XU Zhiping, Ph. D<BR>Civil and Environmental
Engineering<BR>MIT, Cambridge, MA 02139</FONT></DIV></BODY></HTML>