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<br><br>> Date: Tue, 27 Jan 2009 08:46:35 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Segmentation fault with genbox -nmol (version 4.0.3)<br>> <br>> Justin A. Lemkul wrote:<br>> > <br>> > Hi All,<br>> > <br>> > I'm building a system consisting of a protein complex with a few ligands <br>> > free in solution at the outset of the simulation. I'm using genbox -ci <br>> > -nmol to insert the ligands prior to solvation. I'm using version 4.0.3 <br>> > on a dual-core Intel MacBook. The following command fails:<br>> > <br>> > genbox -cp complex_newbox.gro -ci lig.gro -nmol 10<br>> > <br>> > The command works, however, for values of -nmol < 4. The command with <br>> > -nmol 10 works on another machine, an AMD64 Ubuntu box, so this problem <br>> > appears specific to my Mac. Using genbox from version 3.3.3 works just <br>> > fine on the MacBook, and both 4.0.3 and 3.3.3 were built using the same <br>> > compilers (gcc suite, version 4.0.1).<br>> > <br>> > The last few lines of genbox.log from -debug 1 are:<br>> > <br>> > No fcdata or table file name passed, can not read table, can not do <br>> > bonded interactions<br>> > Going to determine what solvent types we have.<br>> > <br>> > ...in case that's helpful. Any ideas why this may have broken, or why <br>> > it may be specific to my Mac?<br>> > <br>> > <br>> > Thanks,<br>> > Justin<br>> > <br>> please enter a bugzilla for this.<br><br>I just ran valgrind on genbox 4.0.4_pre.<br>I get a uninit value warning in check_solvent_cg.<br>I fixed two issues in this part of the code, so it could be that<br>4.0.4 has less problems than 4.0.3.<br>But looking at do_nsgrid it seems that genbox still does not<br>calculate overlap between the inserted molecules,<br>although the output says it does.<br><br>What does genbox do?<br><br>Berk<br><br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<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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