From owner-chemistry@ccl.net Tue Sep 5 18:22:00 2006 From: "Yubo Fan yubofan__mail.chem.tamu.edu" To: CCL Subject: CCL: umbrella sampling using amber 8/9 Message-Id: <-32490-060904215317-9015-pZU31dnbQER9LD3vfBYgSQ*_*server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C6D05B.BA958400" Date: Mon, 4 Sep 2006 19:53:01 -0500 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_000B_01C6D05B.BA958400 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, I am trying to analyze the reaction coordinate using umbrella sampling. = What I want to do is to get the free energy along the reaction coordiate = for ammonia transfer in a protein. This method is not very well = documented in Amber's manual. Is there any similar example available? Or = any advice. Thanks in advance. Sincerely, 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 Dr. Yubo Fan Email: yubofan,+,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_000B_01C6D05B.BA958400 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi, everyone,

I am trying to analyze the reaction = coordinate=20 using umbrella sampling. What I want to do is to get the free energy = along the=20 reaction coordiate for ammonia transfer in a protein. This method is not = very=20 well documented in Amber's manual. Is there any similar example = available? Or=20 any advice. Thanks in advance.

Sincerely,

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
Dr. Yubo=20 Fan &nbs= p; =20 Email: yubofan,+,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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