produce input file , in coarse grained , no standard protein top file
--- 10年5月6日，周四, Justin A. Lemkul <jalem...@vt.edu> 写道： 发件人: Justin A. Lemkul <jalem...@vt.edu> 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" <gmx-users@gromacs.org> 日期: 2010年5月6日,周四,上午10:37 xi zhao wrote: > in fact, how to deal with format problem in coarse-grained ? What do you mean? -Justin > thank you! > > > 4 > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> > > --- *10年5月6日，周四, Justin A. Lemkul /<jalem...@vt.edu>/* 写道： > > > 发件人: Justin A. Lemkul <jalem...@vt.edu> > 主题: Re: [gmx-users] how to show structure results in Martini > coarse-grained simulation? > 收件人: "Gromacs Users' List" <gmx-users@gromacs.org> > 日期: 2010年5月6日,周四,上午9:40 > > > > xi zhao wrote: > > > > Dear Sir : > > The script require what format for top file? my top file is here: > > > > The input is the actual protein topology, not the system topology. > > -Justin > > > ; > > ; Example topology file for MARTINI 2.0 > > ; > > ; First include the file containing all particle definitions, > > ; the interaction matrix, plus the topology for water. > > #include "martini_v2.1.itp" > > #include "martini_v2.0_ions.itp" > > #include "martini_v2.0_lipids.itp" > > #include "3ehz.itp" > > ; Include Position restraint file > > #ifdef POSRES > > #include "s.itp" > > #endif > > [ system ] > > CGprotein ion channel > > [ molecules ] > > ; name number > > Protein 1 > > POPC 502 > > W 18934 > > but run top2psf.pl > > "Cannot open atoms for reading: No such file or directory" > > please help me! > > 4 > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844 > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>> > > > > --- *10年5月3日，周一, Justin A. Lemkul /<jalem...@vt.edu > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道： > > > > > > 发件人: Justin A. Lemkul <jalem...@vt.edu > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>> > > 主题: Re: [gmx-users] how to show structure results in Martini > > coarse-grained simulation? > > 收件人: "Discussion list for GROMACS users" > <gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>> > > 日期: 2010年5月3日,周一,上午8:08 > > > > > > > > xi zhao wrote: > > > Dear user: > > > how to show struture or conformation in Martini coarse-grained > > simulation, using VMD or other? > > > Please give me some suggestion! > > > thank you! > > > > What kind of rendering do you want to do? There are some scripts > > linked below to render bonds in a CG structure. > > > > >http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations > > > > -Justin > > > > > > > > > > > 4 > > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844 > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> > > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844 > ><http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>> > > > > > > > > > > > -- ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- gmx-users mailing list gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org> > > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org> > > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > ><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
