[gmx-users] 4 question

Szilárd Páll szilard.pall at cbr.su.se
Tue Aug 28 22:24:25 CEST 2012

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.


> --
> With The Best
> H.Lanjanian
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