<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Perhaps you can do your parametrization. Enter to the prodrg page and you will see!<br>The page is: <br>http://davapc1.bioch.dundee.ac.uk/prodrg/<br>and you will get your .gro and .top, and you don't need to use the pdb2gmx. If you want to use it anyway, you need to edit the data base, but I think that the manual is not very clear for this item.<br>I think that you should see the .atp they are in the --/gromacs/share/top/ffGxx.atp where xx is the force field that you would use.<br>See your .pdb also and compare the atoms that there are not defined.<br>Cheers.<br>Flor<br><br><br>Dra.M.Florencia Martini<br>
Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas<br>
Cátedra de Química General e Inorgánica<br>
Facultad de Farmacia y Bioquímica<br>
Universidad de Buenos Aires<br>
Junín 956 2º (1113)<br>
TE: 54 011 4964-8249 int 24<br><br>--- El <b>vie 25-sep-09, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> escribió:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>De: Justin A. Lemkul <jalemkul@vt.edu><br>Asunto: Re: [gmx-users] PEO and OPLS-AA FF in gmx<br>Para: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Fecha: viernes, 25 de septiembre de 2009, 12:32 pm<br><br><div class="plainMail"><br><br>lammps lammps wrote:<br>> Hi,<br>> I want to simulate a PEO chain in water using OPLs-AA FF in Gromacs.<br>> I have created a .PDB file using Material Studio, but I seems that the pdb2gmx can not dealt with it because of the error" Residue 'xx' not found in residue topology database"<br>> The question is how can I obtain the .top and .gro file in the framework of OPLS-AA FF. Any suggestion is appreciated.<br>> <br><br>You have to derive
parameters for yourself:<br><br><a href="http://www.gromacs.org/Documentation/How-tos/Parametrization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parametrization</a><br><br>There are a few scripts in the User Contributions section that make efforts to do this for you, but you still have to demonstrate that the parameters are valid.<br><br>-Justin<br><br>> Thanks in advance.<br>> <br>> -- wende<br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a
ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>
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