Thanks Charles. Charles and group: it became a problem in practice for me because I was using the NOE potential for negative PRE restraints on extended chains longer than 99 angstroms. A spin label on one end of the chain will often not enhance the relaxation of many protons at the other end of the chain and this lack of enhancement should be, or has been, used as negative restraints between chain ends. Another nice thing I stumbled upon when using the NOE potential instead of the PRE module is that all the esim functionality is available for ensemble simulations, otherwise I would have had to look more closely into using the method of Iwahara et al.(his scripts are in the python examples) to refine ensembles of structures. There may be some simple clever way to do all this that I'm missing which would make it a non-problem in practice.
David Lowry ----- Original Message ----- From: [email protected]<mailto:[email protected]> To: SUSAN VARNUM<mailto:[email protected]> Cc: [email protected]<mailto:[email protected]> ; [email protected]<mailto:[email protected]> ; [email protected]<mailto:[email protected]> Sent: Tuesday, August 15, 2006 1:47 PM Subject: Re: Speaking of custom energy terms... -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 SUSAN VARNUM <[email protected]<mailto:[email protected]>> wrote: > I've noticed two examples in the literature where folks have used step > potentials rather than "square well" potentials for some of ther > restraints. Is there an easy way to convert the NOE restraint from > square to step? I've been using an ad-hoc solution of setting the > upper bound to 99 angstroms but this is only good for proteins with > extended chains that do not exceed this distance. It does not appear > that I can use a value larger than 99 angstroms because I get an error > message in my out file if I try that. > > > > > With NOE restraint of the form > > > > ( ) ( ) 20.0 0.0 150.0 > > > > I get, in my .out file > > > > NOEPot:addRestraints: error adding restraint > > This is my mistake- it will be fixed in the next release. However, I wonder if this is really a problem in practice? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/<http://mailcrypt.sourceforge.net/>> iD8DBQFE4jLYPK2zrJwS/lYRAq9rAJ9qI3vyGHdNtwaThXw2ro4hVnKeLQCfaVA8 zDRolUkAWnoT8QMZ5V8C9xU= =o/J5 -----END PGP SIGNATURE----- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20060815/0a6ac93f/attachment.html
