on tying "locate ambpdb". I get following output:
/opt/amber10/src/etc/ambpdb.1
/opt/amber10/src/etc/ambpdb.f
/opt/amber10/test/ambpdb
/opt/amber10/test/ambpdb_first_protein
/opt/amber10/test/ambpdb_first_rna
/opt/amber10/test/ambpdb/Run.ambpdb
/opt/amber10/test/ambpdb/prmtop
/opt/amber10/test/ambpdb/restrt
/opt/amber10/test/ambpdb/restrt.pdb.save
/opt/amber10/test/ambpdb_first_protein/Run.ambpdb
/opt/amber10/test/ambpdb_first_protein/first.pdb.save
/opt/amber10/test/ambpdb_first_protein/inpcrd
/opt/amber10/test/ambpdb_first_protein/prmtop
/opt/amber10/test/ambpdb_first_rna/Run.ambpdb
/opt/amber10/test/ambpdb_first_rna/first.pdb.save
/opt/amber10/test/ambpdb_first_rna/inpcrd
/opt/amber10/test/ambpdb_first_rna/prmtop
/opt/amber10/test/nab/dhfrndpmtx.ambpdb
On Tue, Aug 2, 2011 at 2:39 PM, Bruno Rodrigues <bbrodrigues.gmail.com>wrote:
> type
> locate ambpdb
>
> and see if it's somewhere else
>
>
> On Tue, Aug 2, 2011 at 6:07 AM, Bruno Rodrigues <bbrodrigues.gmail.com
> >wrote:
>
> > it seems you set your env $AMBERHOME with a spare slash, so see it
> >
> > /opt/amber10*//*exe/ambpdb
> >
> > there are two slashes after amber10
> >
> >
> > On Tue, Aug 2, 2011 at 12:58 AM, Chirag Vora <chirag740.gmail.com>
> wrote:
> >
> >> I want to generate a PDB file from prmtop file using "ambpdb".
> >>
> >> I execute the following command:
> >> $AMBERHOME/exe/ambpdb -p filename.prmtop < filename.rst > filename.pdb
> >>
> >> It gives an output that says:
> >> bash: /opt/amber10//exe/ambpdb: No such file or directory
> >>
> >> When I see $AMBERHOME/exe/ there is no ambpdb within.
> >>
> >> SUPPLEMENTARY INFORMATION:
> >> OS Ubuntu 10.04 LTS. Amber 10 (parallel). Compiler used for installation
> >> gfortran.
> >>
> >> Should I reinstall Amber or is there a way out?
> >>
> >> --
> >> Chirag V. Vora <chiragvora.live.com>
> >> Department of Pharmacoinformatics<
> >> http://niper.gov.in/depart.htm#Pharmacoinformatics>
> >> ,
> >> National Institute of Pharmaceutical Education and Research<
> >> http://niper.gov.in>
> >> *Sector 67, S.A.S. Nagar, *
> >> *Punjab (INDIA) - 160 062, *
> >> *Phone: +91-9814187740*
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > --
> > Bruno Barbosa Rodrigues
> > PhD Student - Physics Department
> > Universidade Federal de Minas Gerais - UFMG
> > Belo Horizonte - Brazil
> >
>
>
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chirag V. Vora <chiragvora.live.com>
Department of Pharmacoinformatics<http://niper.gov.in/depart.htm#Pharmacoinformatics>
,
National Institute of Pharmaceutical Education and Research<http://niper.gov.in>
*Sector 67, S.A.S. Nagar, *
*Punjab (INDIA) - 160 062, *
*Phone: +91-9814187740*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 02 2011 - 03:00:02 PDT
