From owner-chemistry@ccl.net Thu Nov 29 03:59:01 2007 From: "Tarique Syed Moin tarisyed]|[yahoo.com" To: CCL Subject: CCL:G: Error duing esp calculation having a copper ion in input file Message-Id: <-35735-071129015614-17361-AmWkR+T1F+H5JrNJXTJ9GA::server.ccl.net> X-Original-From: "Tarique Syed Moin" Date: Thu, 29 Nov 2007 01:56:10 -0500 Sent to CCL by: "Tarique Syed Moin" [tarisyed_._yahoo.com] Leave Link 601 at Wed Nov 28 18:28:54 2007, MaxMem= 134217728 cpu: 2.2 (Enter /usr/local/g98/l602.exe) Merz-Kollman atomic radii used. Read replacement radii atom by atom: WANTED AN INTEGER AS INPUT. FOUND A STRING AS INPUT. new_cu_sp_ra.com ? Error termination via Lnk1e in /usr/local/g98/l602.exe. From owner-chemistry@ccl.net Thu Nov 29 14:43:01 2007 From: "Yubo Fan yubofan[a]mail.chem.tamu.edu" To: CCL Subject: CCL: amber score in dock 6.1 Message-Id: <-35736-071129143823-2631-ht0dyurEnJR2VyPJHQunJw ~ server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C8328D.1912D020" Date: Thu, 29 Nov 2007 13:38:17 -0600 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan^^mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C8328D.1912D020 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I have a question about setting the flexible region for docking with = UCSF Dock 6.1. If I need to set the ligand and certain amino acid residues as movable = region, how can I define them. For example, how can I set the ligand and = residue 20-30 movable for docking in the keyword shown below? amber_score_movable_region [ligand] (distance, everything, ligand, = nab_atom_expression, nothing): Thanks a lot, Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Yubo Fan Ph.D Email: yubofan*o*mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_000D_01C8328D.1912D020 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello,
 
I have a question about setting the = flexible region=20 for docking with UCSF Dock 6.1.
 
If I need to set the ligand and certain = amino acid=20 residues as movable region, how can I define them. For example, how can = I set=20 the ligand and residue 20-30 movable for docking in the keyword shown=20 below?
amber_score_movable_region [ligand] (distance, everything, ligand,=20 nab_atom_expression, nothing):
Thanks a lot,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Yubo=20 Fan =20 Ph.D           &nb= sp;=20 Email: yubofan*o*mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
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