Dear Sir : The script require what format for top file? my top file is here:
; ; 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! --- 10年5月3日，周一, 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: "Discussion list for GROMACS users" <gmx-users@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> > > > -- ======================================== 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
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