From owner-chemistry@ccl.net Sat May 2 11:35:00 2009 From: "Bruno Andrade bandradefsa**yahoo.com.br" To: CCL Subject: CCL: Energy minimization and Molecular Dynamics with Heme Group Message-Id: <-39220-090501225508-15260-WGjVCRvdpdQjs7YULJcHcw],[server.ccl.net> X-Original-From: "Bruno Andrade" Date: Fri, 1 May 2009 22:55:04 -0400 Sent to CCL by: "Bruno Andrade" [bandradefsa.:.yahoo.com.br] Dear CCL subscribers, I'm trying to perform an energy minimization and after a molecular dynamics using AMBER 9.0, and my protein has a Heme group. So, I think AMBER doesnt have parameters to calculate a heme group, because it returs me an error message or the program kills the job. am I wrong? is there any other program I can use to? Thank you for your help. Sincerely, Bruno Andrade. From owner-chemistry@ccl.net Sat May 2 14:24:01 2009 From: "Marcel Swart marcel.swart\a/icrea.es" To: CCL Subject: CCL: Energy minimization and Molecular Dynamics with Heme Group Message-Id: <-39221-090502142221-740-y61vv+pQ8sfQ2u9ulwMnXw:server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 2 May 2009 20:19:09 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.es] See the contributed parameter sets within Amber: http://www.pharmacy.manchester.ac.uk/bryce/amber Note also the paper in J. Comput. Chem. with the title "New AMBER Force Field Parameters of Heme Iron for Cytochrome P450s Determined by Quantum Chemical Calculations of Simplified Models" J Comput Chem 26: 818 - 826, 2005 Quoting "Bruno Andrade bandradefsa**yahoo.com.br" : > > Sent to CCL by: "Bruno Andrade" [bandradefsa.:.yahoo.com.br] > Dear CCL subscribers, > > I'm trying to perform an energy minimization and after a molecular =20 > dynamics using AMBER 9.0, and my protein has a Heme group. So, I =20 > think AMBER doesnt have parameters to calculate a heme group, =20 > because it returs me an error message or the program kills the job. =20 > am I wrong? is there any other program I can use to? > > Thank you for your help. > > Sincerely, > > Bruno Andrade. > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=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. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart:-:icrea.es marcel.swart:-:udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Sat May 2 14:59:01 2009 From: "Prashant Kumar prashantkbio()gmail.com" To: CCL Subject: CCL: Energy minimization and Molecular Dynamics with Heme Group Message-Id: <-39222-090502143458-5293-n00+Rkv0puiljsa5u3KXIw[-]server.ccl.net> X-Original-From: Prashant Kumar Content-Type: multipart/alternative; boundary=000e0cd5194ee7c7940468f22e33 Date: Sun, 3 May 2009 00:04:30 +0530 MIME-Version: 1.0 Sent to CCL by: Prashant Kumar [prashantkbio]|[gmail.com] --000e0cd5194ee7c7940468f22e33 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Bruno, I guess you haven't generated the frcmod abd prepin file for heme group. Use antechamber for this and then by using leap generate the crd and top file for input for sander. Regards -- Prashant On Sat, May 2, 2009 at 8:25 AM, Bruno Andrade bandradefsa**yahoo.com.br < owner-chemistry%x%ccl.net> wrote: > > Sent to CCL by: "Bruno Andrade" [bandradefsa.:.yahoo.com.br] > Dear CCL subscribers, > > I'm trying to perform an energy minimization and after a molecular dynamics > using AMBER 9.0, and my protein has a Heme group. So, I think AMBER doesnt > have parameters to calculate a heme group, because it returs me an error > message or the program kills the job. am I wrong? is there any other program > I can use to? > > Thank you for your help. > > Sincerely, > > Bruno Andrade.> > > --000e0cd5194ee7c7940468f22e33 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Bruno,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I guess = you haven't generated the frcmod abd prepin file for heme group. Use an= techamber for this and then by using leap generate the crd and top file for= input for sander.
Regards
--
Prashant

On Sat, May 2, 2009 at 8:= 25 AM, Bruno Andrade bandradefsa**yahoo.com= .br <ow= ner-chemistry%x%ccl.net> wrote:

Sent to CCL by: "Bruno =A0Andrade" [bandradefsa.:.yahoo.com.br]
Dear CCL subscribers,

I'm trying to perform an energy minimization and after a molecular dyna= mics using AMBER 9.0, and my protein has a Heme group. So, I think AMBER do= esnt have parameters to calculate a heme group, because it returs me an err= or message or the program kills the job. am I wrong? is there any other pro= gram I can use to?

Thank you for your help.

Sincerely,

Bruno Andrade.



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