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Hi,<br><br>This is a known bug in 4.0.<br>It has been fixed for 4.0.1, which will hopefully be released today.<br><br>Berk<br><br><br>> Date: Fri, 7 Nov 2008 11:23:14 +0100<br>> From: caterina.arcangeli@casaccia.enea.it<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] editconf/genbox problem in Gromacs 4.0<br>> <br>> Dear gmx-users,<br>> <br>> I have encountered a similar editconf/genbox problem posted by Matt<br>> Danielson on 14 October:<br>> I 'm using Gromacs 4.0 (installed on MacOS).<br>> <br>> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o may_protein_box.pdb<br>> <br>> The output from editconf does not report errors, but I noted that the<br>> volume of the box is 0!<br>> <br>> ----------- output message-------------------------------<br>> WARNING: masses will be determined based on residue and atom names,<br>> this can deviate from the real mass of the atom type<br>> Entries in atommass.dat: 178<br>> WARNING: vdwradii will be determined based on residue and atom names,<br>> this can deviate from the real mass of the atom type<br>> Entries in vdwradii.dat: 28<br>> Entries in dgsolv.dat: 7<br>> Entries in electroneg.dat: 71<br>> Entries in elements.dat: 218<br>> Read 16824 atoms<br>> Volume: 0 nm^3, corresponds to roughly 0 electrons<br>> -----------------------------------------------------------------<br>> <br>> 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro -o<br>> my_protein_wat.pdb -p my_protein.top<br>> <br>> The output from genbox_d reports the following error:<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>> <br>> I have performed the same commands on another machine (Linux) running<br>> version 3.3 and I produced with success a nice solvent box.<br>> <br>> Suggestions?<br>> <br>> Thanks,<br>> Caterina<br>> <br>> <br>> <br>> -- <br>> Caterina Arcangeli<br>> ENEA, Dept. Physics (FIM-CAMO)<br>> C.R. Casaccia, SP 026<br>> Via Anguillarese 301 - 00123 Roma<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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