[gmx-users] 4 question

[Hossein Lanjanian]

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.

-- 
With The Best
H.Lanjanian