[gmx-users] 4 question

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Aug 17 19:33:46 CEST 2012


The .pdb file either should be dowloaded from RCSB website or you need to construct the structure by a software such as hyperchem and save the structure in .pdb format, so you are not supposed to get .pdb output through pdb2gmx command.

About the second problem, I think you need to chose the proper -ter. I've experienced these problem before and that was the problem. However I have not done the tutorial . Here others might help you better.

In my person, OpenSuse and Ubuntu are proper options.


From: Hossein Lanjanian <hossein.lanjanian at gmail.com>
To: gmx-users at gromacs.org 
Sent: Friday, August 17, 2012 9:49 PM
Subject: [gmx-users] 4 question


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
your kind guidance is appreciated in advance.

With The Best
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