From chemistry-request@server.ccl.net Thu Apr 11 17:42:07 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3BLg7j25211 for ; Thu, 11 Apr 2002 17:42:07 -0400 Received: from mailscan-out2.cac.washington.edu (mailscan-out2.cac.washington.edu [140.142.33.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g3BLfw8J003944 for ; Thu, 11 Apr 2002 14:41:59 -0700 Received: FROM homer38.u.washington.edu BY mailscan-out2.cac.washington.edu ; Thu Apr 11 14:41:57 2002 -0700 Received: from localhost (xjtan@localhost) by homer38.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g3BLfrfI113216 for ; Thu, 11 Apr 2002 14:41:57 -0700 Date: Thu, 11 Apr 2002 14:41:53 -0700 (PDT) From: "X. Tan" To: chemistry@ccl.net Subject: torsion constraints in autodock Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I'd like to ask you a question about torsion constraints. I have a set of small molecules with the peptide bonds(CO-NH) attaching to a benzene ring. In principle, all the atoms in peptide bonds and benzene should be almost coplanar. In another word, the bond between peptide bond and benzene ring should has the torsion angel either 0 or 180 degree. When I did autodock computation without torsion constraint on this kind of bonds, it gave me the answers with the torsion angel about 90 degree. Later, I used "hardtorcon" on these bonds. The conformations I got were still not good, with the torsion angel about 60 degree. Here is one of my pdbq file, ---------------------- REMARK 12 active torsions (identified by new id numbers): REMARK status: ('A' for Active; 'I' for Inactive) REMARK I 1- 14 between atoms: C1 and O30 REMARK 1 A 2- 16 between atoms: C2 and O3 REMARK 2 A 16- 17 between atoms: O3 and C4 REMARK 3 A 19- 20 between atoms: C10 and C11 REMARK 4 A 22- 24 between atoms: N13 and C15 REMARK 5 A 24- 25 between atoms: C15 and C16 REMARK 6 A 25- 26 between atoms: C16 and C17 REMARK 7 A 26- 27 between atoms: C17 and N32 REMARK 8 A 36- 37 between atoms: C6 and N7 REMARK 9 A 39- 41 between atoms: C40 and C41 REMARK 10 A 41- 42 between atoms: C41 and O42 REMARK 11 A 42- 43 between atoms: O42 and C43 REMARK 12 A 43- 44 between atoms: C43 and C45 REMARK I 4- 5 between atoms: C20 and C21 REMARK I 5- 6 between atoms: C21 and O22 REMARK I 8- 9 between atoms: C24 and O25 REMARK I 11- 12 between atoms: C27 and O28 ROOT ... -------------------- For this molecule, I defined the torsion constaints like this: hardtorcon 3 0. 10. # constrain torsion, num., angle(deg), range(deg) hardtorcon 8 0. 10. # constrain torsion, num., angle(deg), range(deg) I wondered whether I gave the wrong constraint. For a torsion A-B-C-D, in autodock program, the rotatable bond is defined by two atoms(B-C), then where the A and D come from, and is it possible to assign the torsion angle unambiguously in the constraints? How to do that? BTW, I have another question about autodock. Atom F is a stronger H-Bond acceptor, but why there is no H-Bond parameters for F in autodock(I used version 3.03)? Any help would be greatly appreciated! Xiaojian Tan xjtan@u.washington.edu