[gmx-users] Initial Conformation Generation

[Andreas Kukol]

>>> gauravp at che.iitb.ac.in 01/10/2004 12:26:16 >>>
Dear all,

This query is not directly related to Gromacs but is being posted here
because it is in a related area.

I'll be very grateful if somebody can please let me know of a good
software (URL etc.) which can generate initial random structures from a
given amino acid sequence based on secondary structure predictions i.e.
helices and sheets should appear in the initial structures which can then 
be subject to MD and other analysis.

Thank you.

Regards,
Gaurav


A (free) software for initial structure generation is Biomer or B:

http://www.scripps.edu/mb/case/Biomer/

You can add residue after residue with specified secondary structure by a mouseclick, which might be tedious for a long sequence. Structure editors of commercial software like Hyperchem or Quanta do a similar job.

Regards
Andreas