Thanx for your nice comment On Aug 29, 2012 12:54 AM, "Szilárd Páll" <szilard.p...@cbr.su.se> wrote:
> On Fri, Aug 17, 2012 at 7:19 PM, Hossein Lanjanian > <hossein.lanjan...@gmail.com> wrote: > > Hi > > > > we are new academic users of GROMACS. we installed gromacs 4.5.5 and > > tried to learn the job by using tutorials found in the "gromacs.org" > > web site. There is one question: > > we successfully ran the "1PGB.pdb". > > we know that *.pdb or *.gro files are necessary for the rest of > > analysis however we have not been able to get either of these two > > outputs from the first command " pdb2gmx -f 1PGB.pdb -ter ......" > > how is it possible?? > > > > Also we were trying to run membrane-receptor simulation, so we used > > gromacs.org tutorial again. according to that we got the "B2AR" > > protein but there were two problems with capping this protein: > > 1- when we ran the first command "pdb2gmx -f B2AR.pdb -o > > B2AR_processed.gro -ignh -ter " and chose the gromos96ff43a1" > > force-field and SPC water, the following error appeared: > > "there is a dangling bound at at least one of the terminal ends. > > select a proper terminal entry." > > when we omitted the "-ter" the error message changed to > > "there were 3 missing atoms in molecule protein_chain_A, if you want > > to use this incomplete topology anyhow, use the option -missing" > > after using "-missing" we encountered the following message > > "Residue 'MAL' not found in residue topology database" > > 2- there is no [ molecules ] section in the topology file, to modify > > as mentioned in the section two of tutorial. > > > > In the end: > > We have run GROMACS in different distributions of Linux such as > > Redhat, Centos and mint, nonetheless, which distribution do you > > recommend? > > your kind guidance is appreciated in advance. > > As it's been mentioned, if getting the highest performance possible is > not of utmost importance, the best distribution is the one that you > like the most. > > >From the point of view of performance, the distribution doesn't matter > much either. What matters is the compiler and in some cases the OS > kernel version. For instance, on new hardware the difference between > using and old vs newer gcc version can be up to 20%, so use recent > compilers whenever you can. > > -- > Szilárd > > > -- > > With The Best > > H.Lanjanian > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists