Charles, Thank you very much for your reply.
I have built my small molecule with XPLOR, so now I have both psf and pdb files. In general, to perform a simulated annealing for the complex of protein and small molecule do I have to keep a small molecule rigid to get it in proper orientation and without distorsion of its structure? Thank you, Irina. ----- Original Message ----- From: <[email protected]> To: "Irina Nesmelova" <nesme001 at umn.edu> Cc: <Charles at Schwieters.org> Sent: Friday, January 04, 2008 2:10 PM Subject: Re: [Xplor-nih] structure of protein with ligand > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Irina-- > >> I want to calculate a structure of protein dimer, in which each of the >> monomers has ligand - non-peptidic small molecule. I have a pdb file >> for ligand. How should I the information about ligand into python >> script? > > You will need PSF information for the ligand. You might read: > > http://nmr.cit.nih.gov/xplor-nih/faq.html#node0150.txt > > I intend to create a facility to deal with rigid small molecules (given > a pdb), but haven't managed to do so yet. > > For a dimer you'll also want to use the NCS potential term. For that, > add this bit to your Python script: > > #non-crystallographic symmetry - so that each monomer is > # (more or less) identical > xplor.command(""" > ncs restraints > initialize > group > equi (segid A) > equi (segid B) > weight = 1 > end > ? > end""") > potList.append( XplorPot('NCS') ) > rampedParams.append( MultRamp(.01,10,"potList['NCS'].setScale(VALUE)") ) > > hope this helps-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iD8DBQFHfpKiPK2zrJwS/lYRAlq1AKCJYw21d1dH4DfgNVb8U9wD09UhfQCdEFRY > jkmoRGNYahOeqpz1ysQ40Hk= > =GX+U > -----END PGP SIGNATURE----- >
