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Hi,<br><br>Indeed this bug has been fixed in 4.0.2.<br><br>Berk<br><br>> Date: Mon, 24 Nov 2008 11:00:46 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] problem in gromacs 4?<br>> <br>> Several users have reported this problem, i.e.:<br>> <br>> http://www.gromacs.org/pipermail/gmx-users/2008-November/038181.html<br>> <br>> Perhaps try upgrading to version 4.0.2 and try again.<br>> <br>> -Justin<br>> <br>> Bernhard Knapp wrote:<br>> > Dear users<br>> > <br>> > I am trying to minimize the energy of a complex using gromacs 4. The <br>> > commands are the following:<br>> > <br>> > pdb2gmx -f full_mCARKL_to_xylose_kinaseFH.pdb -o <br>> > full_mCARKL_to_xylose_kinaseFH.gro.pdb -p <br>> > full_mCARKL_to_xylose_kinaseFH.top -ignh<br>> > editconf -f full_mCARKL_to_xylose_kinaseFH.gro.pdb -o <br>> > full_mCARKL_to_xylose_kinaseFH.cube.pdb -bt cubic -d 2.0<br>> > genbox -cp full_mCARKL_to_xylose_kinaseFH.cube.pdb -cs spc216.gro -o <br>> > full_mCARKL_to_xylose_kinaseFH.water.pdb -p <br>> > full_mCARKL_to_xylose_kinaseFH.top -nice 0<br>> > <br>> > after genbox it stops with the error<br>> > <br>> > -------------------------------------------------------<br>> > Program genbox, VERSION 4.0<br>> > Source code file: gmx_genbox.c, line: 744<br>> > <br>> > Fatal error:<br>> > Undefined solute box.<br>> > Create one with editconf or give explicit -box command line option<br>> > -------------------------------------------------------<br>> > <br>> > Although this is definitly not true since the box has been created with <br>> > editconf (and not error is given by it). If I try the same commands (and <br>> > complex) on Gromacs 3.3 it works fine without error. Any ideas?<br>> > <br>> > Thank you in advance<br>> > Bernhard<br>> > <br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www <br>> > interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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