[gmx-users] 4 question

[Hossein Lanjanian]

Thank you justin for your kindly response
On Aug 17, 2012 9:56 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>
> On 8/17/12 1:19 PM, H
>
>
>
> 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:
>
> http://www.gromacs.org/**Documentation/Errors#pdb2gmx<http://www.gromacs.org/Documentation/Errors#pdb2gmx>
>
>  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
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<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<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<http://www.gromacs.org/Support/Mailing_Lists>
>