[gmx-users] 4 question

[Hossein Lanjanian]

Thanx for your nice comment
On Aug 29, 2012 12:54 AM, "Szilárd Páll" <szilard.pall at cbr.su.se> wrote:

> On Fri, Aug 17, 2012 at 7:19 PM, Hossein Lanjanian
> <hossein.lanjanian at 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 at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>