[gmx-users] 4 question

Justin Lemkul jalemkul at vt.edu
Fri Aug 17 19:24:32 CEST 2012

On 8/17/12 1:19 PM, Hossein Lanjanian 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??

If pdb2gmx failed, it will have produced an error message.  Just about 
everything you might encounter is described here:


> 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."

Are capping groups present in the input .pdb file?  If not, you need to build 
them on using some external software.  Gromacs by default only treats 
protonation state of termini with limited ability to build on atoms (described 
in .n.tdb and .c.tdb files).

>   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

It is almost always incorrect to use the -missing flag.  Your model needs to be 
intact to proceed, otherwise the topology is almost always garbage.

> "Residue 'MAL' not found in residue topology database"

pdb2gmx is not magic.  See the link above.

> 2- there is no [ molecules ] section  in the topology file, to modify
> as mentioned in the section two of tutorial.

You shouldn't move to step 2 if step 1 is failing ;)

> In the end:
> We have run GROMACS in different distributions of Linux such as
> Redhat, Centos and mint, nonetheless, which distribution do you
> recommend?

For desktop usage, use whatever distribution you find most convenient.  Gromacs 
will run on just about anything.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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