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