From chemistry-request@server.ccl.net Fri Jan 3 15:23:03 2003 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h03KN3002617 for ; Fri, 3 Jan 2003 15:23:03 -0500 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (/8.10.1) with ESMTP id h03KN1sE004134; Fri, 3 Jan 2003 15:23:01 -0500 (EST) Date: Fri, 3 Jan 2003 14:15:21 -0500 From: Rick Venable To: tluchko cc: chemistry@ccl.net Subject: Re: CCL:CHARMM: GTP and GDP parameters In-Reply-To: <3E165239@webmail.ualberta.ca> Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is a simple editing bug, and should be fixed in the next parameter release. To correct the problem: in ATP or ADP change the following atom types ATOM C2' CN7 0.14 ! to ATOM C2' CN7B 0.14 ! and ATOM C5' CN8 -0.08 to ATOM C5' CN8B -0.08 On Thu, 2 Jan 2003, tluchko wrote: > I am trying to come up with some parameters for GTP and GDP bound to > tubulin for the CHARMM27 parameter set. My hope is to use ATP and > ADP as a starting point, however, I have run into two problems. > The first is that CHARMM does not seem to like the ATP/ADP > parameters themselves. I get errors such as > > : No angle parameters for 5 ( ON6B CN7 CN8 ) > : A TOTAL OF 5 MISSING PARAMETERS > > ***** LEVEL -1 WARNING FROM ***** > ***** CODES> MISSING PARAMETERS > ****************************************** > BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5 > > CHECKDH> dihedral : 1 28 31 32 will NOT be generated > > Is there something wrong with the parameters? If these parameters are > supposed to be missing for ADP/ATP why is this correct? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=