Dear sir: Thank you for your help!
--- 10年4月11日，周日, shaya...@post.tau.ac.il <shaya...@post.tau.ac.il> 写道： 发件人: shaya...@post.tau.ac.il <shaya...@post.tau.ac.il> 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: jalem...@vt.edu, "Discussion list for GROMACS users" <gmx-users@gromacs.org> 日期: 2010年4月11日,周日,下午10:01 Dear Xi Zhao, For inserting protein into membrane you might like to try use g_membed (link http://wwwuser.gwdg.de/~ggroenh/membed.html) This is not strictly (yet) a gromacs package, but it can be very easily be complied and used per instructions of the authors. Technically, the package 'compress' the protein to be a linear line, then inserts it into the membrane and starts 'pumping' it back to the original size. Hope that help, -Shay Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > > > xi zhao wrote: >> I would like to run a simulation of a pentamers in a POPC membrane, and >> using new inflategro with doughnut mode, but I have met similar result as >> the links >> http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I >> also <http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html >> ,I also> got a lot of errors about uninitialized values. When the script >> finishes, the membrane is rescaled, but the protein is untouched in the >> corner of the new box. Please give me some suggestions! Thank you in >> advance! >> > best regards! > > I think the problem comes from pattern matching in the script. With large > bilayers, the atom names and numbers will not be split correctly; this could > be causing a problem for you. I'd again suggest that you contact the > developer of the program and discuss this issue, as it is not really a > Gromacs problem and only a few people on this list really use such programs. > I think you'll find a resolution faster that way. > > -Justin > >> >> >> >> 4 >> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> >> >> --- *10年4月9日，周五, Justin A. Lemkul /<jalem...@vt.edu>/* 写道： >> >> >> 发件人: Justin A. Lemkul <jalem...@vt.edu> >> 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation >> 收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >> 日期: 2010年4月9日,周五,上午2:14 >> >> >> >> xi zhao wrote: >> > >> > >> > Dear sir : >> > I want to a pentamer membrane protein, when I used InflateGRO.pl >> with /DOUGHNUT Mode, the results were wrong, please help me! / >> >> If you want any useful help, you'll have to do a whole lot better >> than simply saying "the results were wrong." No one on this list >> will have any idea what you mean. If you believe there is some >> error in the script itself, you're better off contacting its author. >> >> -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>>show >> " [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 >> POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits >> > Doughnut mode activated. Protein coordinates will be translated >> by subunit .... >> > Reading..... >> > Reading chain identifiers.... >> > Subunit 1: atom 1 to atom 3238 >> > Subunit 2: atom 3239 to atom 6476 >> > Subunit 3: atom 6477 to atom 9714 >> > Subunit 4: atom 9715 to atom 12952 >> > Subunit 5: atom 12953 to atom 16190 >> > There are 5 protein subunits.... >> > Scaling lipids.... >> > There are 512 lipids... >> > with 65 atoms per lipid.. >> > Determining upper and lower leaflet... >> > 256 lipids in the upper... >> > 256 lipids in the lower leaflet >> > Checking for overlap.... >> > ...this might actually take a while... >> > ....... >> > Argument "N4" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C5" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C6" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "O7" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "P8" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "O9" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "A1" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "A2" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C1" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C2" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C3" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "N4" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C5" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "C6" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "O7" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "P8" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "O9" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "A1" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Argument "A2" isn't numeric in printf at inflategro.txt line 708, >> <CHAINS> line 5. >> > Calculating Area per lipid... >> > Protein X-min/max: 23 105 >> > Protein Y-min/max: 18 100 >> > X-range: 82 A Y-range: 82 A >> > Building 82 X 82 2D grid on protein coordinates... >> > Calculating area occupied by protein.. >> > full TMD.. >> > upper TMD.... >> > lower TMD.... >> > Area per protein: 49 nm^2 >> > Area per lipid: 9.83158146861789 nm^2 >> > Area per protein, upper half: 38.75 nm^2 >> > Area per lipid, upper leaflet : 9.79362516645161 nm^2 >> > Area per protein, lower half: 45.75 nm^2 >> > Area per lipid, lower leaflet : 9.92548787409836 nm^2 >> > Writing Area per lipid... >> > Done! >> > >> > >> > -- ======================================== >> >> 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? 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