[gmx-users] Initial Conformation Generation

[Anton Feenstra]

Andreas Kukol wrote:

>>>>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.
[...]
> 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.

The non-commercial modeling program 'WhatIf' can do it as well, it should
either be free for academics, or available at a reasonable fee.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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