From owner-chemistry@ccl.net Tue Oct 2 08:27:00 2012 From: "lakshmi maganti lakshmimaganti6-$-gmail.com" To: CCL Subject: CCL: Query Message-Id: <-47696-121001095130-20839-71PbPOnRvbArXKVTXhle1w*o*server.ccl.net> X-Original-From: "lakshmi maganti" Date: Mon, 1 Oct 2012 09:51:28 -0400 Sent to CCL by: "lakshmi maganti" [lakshmimaganti6__gmail.com] I am working as a research student .I have query regarding MD simulation.I wanted to perform MD simulation on a protein.That protein is in monomer in case of apo form and tetramer in case of ligand bound form. four ligands(same structure) are bound to four chains.Wether i can continue my MD on monomer both in case of ligand bound and without ligand bound.please suggest me . Thanking you From owner-chemistry@ccl.net Tue Oct 2 10:15:00 2012 From: "Gerard Pujadas gerard.pujadas/./gmail.com" To: CCL Subject: CCL: FoldX: doubt on the meaning of the output of the PositionScan command Message-Id: <-47697-121002101142-10986-TJhKZTvju9eVU0Z9o8volQ _ server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=047d7b339c4d54f80004cb14195e Date: Tue, 2 Oct 2012 16:11:31 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas]=[gmail.com] --047d7b339c4d54f80004cb14195e Content-Type: text/plain; charset=ISO-8859-1 Dear CCL subscribers, I have some doubts about the meaning of the output files for the FoldX's PositionScan command ... My first question is on the meaning of the different columns at the energies files. As you can see at the next example at the FoldX website ( http://foldx.crg.es/examples/positionscan/energies_39_1shg.txt), there are more columns than the number of contributions to the FoldX's force field and in the manual I have no found how to interpret them ... Which is also the meaning of the http://foldx.crg.es/examples/positionscan/scanning_output.txt file? I have asked both question to the e-mail that appears at the FoldX website but without any answer ... May you be so kind to help me? With many thanks in advances Yours sincerely Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group phone +34 977 55 (9565) Biochemistry and Biotechnology Department Office 106, Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia --047d7b339c4d54f80004cb14195e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL subscribers,

I have some doubts about the meaning of th= e output files for the FoldX's PositionScan command ...

My first= question is on the meaning of the different columns at the energies files.= As you can see at the next example at the FoldX website (http://foldx.crg.es/examples/positionscan/energies_39_1shg.txt), there= are more columns than the number of contributions to the FoldX's force= field and in the manual I have no found how to interpret them ...

Which is also the meaning of the http://foldx.crg.es/e= xamples/positionscan/scanning_output.txt file?

I have asked both= question to the e-mail that appears at the FoldX website but without any a= nswer ...

May you be so kind to help me?

With many thanks in advances
<= br>Yours sincerely

Gerard

--
Gerard Pujadas
http://bioquimica= .urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Office 106, Building N4, Campu= s Sescelades
Universitat Rovira i Virgili
Tarragona, Catalonia=

--047d7b339c4d54f80004cb14195e-- From owner-chemistry@ccl.net Tue Oct 2 12:03:01 2012 From: "Venable, Richard (NIH/NHLBI) E venabler_-_nhlbi.nih.gov" To: CCL Subject: CCL: Query Message-Id: <-47698-121002120012-14140-7WkurxNLOk0pQmSFRb52Yg() server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 2 Oct 2012 11:59:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler^^nhlbi.nih.gov] The information presented suggests that structural differences between the monomer and tetramer ought to be part of the study. It also depends on what is known about the event order, i.e. which occurs first; binding, or tetramer formation? Some simulation packages (e.g. CHARMM) allow the user to simulate the tetramer through symmetry, rather than requiring all 4 monomers; the risk is that differences between subunits in the tetramer are disallowed. Doing the tetramer both ways can be informative about the role of symmetry. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 10/1/12 9:51 AM, "lakshmi maganti lakshmimaganti6-$-gmail.com" wrote: > >Sent to CCL by: "lakshmi maganti" [lakshmimaganti6__gmail.com] >I am working as a research student .I have query regarding MD >simulation.I wanted to perform MD simulation on a protein.That protein is >in monomer in case of apo form and tetramer in case of ligand bound form. > four ligands(same structure) are bound to four chains.Wether i can >continue my MD on monomer both in case of ligand bound and without ligand >bound.please suggest me . > >Thanking you