Hi yes I do use genion and g_rdf properly with 4.0.2 Regards
and Sampo Karkola wrote: > Hi, > > so you got genion working with 4.0.2? > > Sampo > > andrea spitaleri wrote: >> gcc-4.0.2 seems ok for gmx-3.3.1 >> I have also submitted in bugzilla a similar problem with g_rdf >> >> >> Regards >> >> andrea >> >> Sampo Karkola wrote: >>> Hi, >>> >>> the same one, gcc-4.1. Have you tried with other versions? >>> >>> Sampo >>> >>> andrea spitaleri wrote: >>>> Hi >>>> which gcc have you used for compiling gromacs? I have the same problem >>>> in one pc in which I have >>>> build gromacs using gcc-4.1 >>>> >>>> Regards >>>> >>>> andrea >>>> >>>> Sampo Karkola wrote: >>>>> Dear list, >>>>> >>>>> the genion program gets halted when I'm trying to replace the solvent >>>>> molecules with ions. The command >>>>> >>>>> genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top >>>>> -pname NA+ -nname CL- -random -neutral -conc 0.1 >>>>> >>>>> asks for the group of solvent molecules and when I tell him to use >>>>> it I >>>>> get this output >>>>> >>>>> Selected 12: 'SOL' >>>>> Number of (3-atomic) solvent molecules: 9918 >>>>> >>>>> Processing topology >>>>> Replacing 9875 solute molecules in topology file (fdt.top) by 22 NA+ >>>>> and 21 CL- ions. >>>>> >>>>> Back Off! I just backed up fdt.top to ./#fdt.top.2# >>>>> Replacing solvent molecule 1163 (atom 6250) with NA+ >>>>> >>>>> and then nothing happens. genion.log gets generated only half way. My >>>>> system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via >>>>> synaptic and also built from source. The same thing happens in both of >>>>> them. Gromacs version is 3.3.1. However, when I try the same thing on >>>>> another machine, a HP Proliant ML350 with Debian Sarge and Gromacs >>>>> 3.3.1, everything goes well. >>>>> >>>>> None of the gromacs programs gives any errors before genion. >>>>> >>>>> I'll give you more info about the system configuration if anyone >>>>> asks :) >>>>> >>>>> Sampo >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>> interface or send it to [EMAIL PROTECTED] >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php