[gmx-users] Initial Conformation Generation
feenstra at few.vu.nl
Mon Oct 4 08:18:44 CEST 2004
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:
> 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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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