[gmx-users] 4 question

[Hossein Lanjanian]

Thank you Shima for your kindly response
On Aug 17, 2012 10:05 PM, "Shima Arasteh" <shima_arasteh2001 at yahoo.com>
wrote:

> Hi,
>
> 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.
>
>
>
>
> Sincerely,
> Shima
>
>
> ________________________________
> 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
>
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 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
>