From chemistry-request # - at - # server.ccl.net Wed Feb 6 10:29:14 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g16FTEc28081 for ; Wed, 6 Feb 2002 10:29:14 -0500 Received: from localhost (rvenable[ AT ]localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA68724; Wed, 6 Feb 2002 10:21:21 -0500 (EST) Date: Wed, 6 Feb 2002 10:21:21 -0500 From: Rick Venable To: songyunlong cc: "chemistry %-% at %-% ccl.net" Subject: Re: CCL:Charmm22 force field for DNA In-Reply-To: <20020206105618.D25181E303981 -x- at -x- smtp.263.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 5 Feb 2002, songyunlong wrote: > Recently,I met with a difficult problem.I want to run a MCSS job to > investigate the active site of a protein-DNA complex.However,the > MCSS job requires the force field must be charmm22 force field. Then > I assign the charmm22 force field to the protein-DNA > complex,however,some nitrogen atoms of DNA,such as N3,N7, are not > parameterized by charmm22 force field.I wonder whether DNA has been > parameterized by charmm22 force field.In my opinion,as a famous > macromolecular force field,CHARMM should have parmaterized for DNA > as well as protein.How can I settle this problem? How can I > parameterize DNA with charmm22 force field? Could you please kindly > give me any suggestions on this problem? The latest versions of the CHARMM academic parameters can be found at http://www.pharmacy.umaryland.edu/~alex/research.html There is a specific protein:nucleic acid set of matched RTF and PARAM files for use in studies of this type; it has existed for some time, and has been distributed with CHARMM since about 1995. Note that "charmm22 force field" is often a minimum requirement; it refers in general to the introduction of an "all atom" force field, including non-polar (aliphatic, etc.) H atoms. Other force fields such as GROMACS omit these atoms, as did CHARMM prior to version 22. For MCSS calculations, you may wish to use the most recent version of the "prot_na" files, found at the above URL. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable;at;nih.gov ALT email: rvenable ^at^ speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=