Have you ever look at acpype.googlecode.com?
Alan
On 14 October 2011 08:48, madhumita das <madhumita.bioinfo.gmail.com> wrote:
> Dear Ivan,
> Thanks for your suggestion. I tried according to your
> suggestion but the same error comes. since the bash command doesn't work
> properly in my computer, I have made a source file to run under csh
> command,the contents of that file are
> setenv AMBERHOME /usr/local/amber11
> set PATH =( $AMBERHOME/bin:$PATH )
> and the I ran ./ambgmx.pl but the same error comes, it couldn't find the
> ambpdb and rdparm commands.
>
> please help me.
>
> Madhumita Das
>
> On Fri, Sep 30, 2011 at 2:01 PM, madhumita das
> <madhumita.bioinfo.gmail.com>wrote:
>
> > Hi amber users,
> >
> > I have generated prmtop and inpcrd files for a residue and I want to
> > convert it top and gro files needed for gromacs,but whenever I run the
> > command
> > ./amb2gmx.pl -prmtop peptide.prmtop -crd peptide.prmcrd -outname lambda
> > following error comes
> > ambpdb: command not found
> > rdparm: command not found
> > Parsing PDB file lambda.pdb...
> > found:
> > 0 protein residues
> > 0 sodium ions
> > 0 chloride ions
> > 0 waters
> >
> > Use of uninitialized value in printf at ./amb2gmx.pl line 263.
> > 0 TOTAL residues read
> > Reading prmtop file...
> > 0 atom type indices read.
> >
> > found:
> > 0 atoms
> > 0 bonds
> > 0 angles
> > 0 torsions
> >
> > Qtot = 0
> > Qmax = 0 at atom -1
> >
> > Constructing list of unique nonbonded atomtypes...
> > 0 unique atomtypes found.
> > Writing atom types...
> > Done.
> > sh-3.1# export AMBERHOME=/root/Desktop/SEEMA_YADAV/amber11sh-3.1# export
> > PATH=$AMBERHOME/exe:$PATHsh-3.1# ./amb2gmx.pl -prmtop peptide.prmtop
> -crd
> > peptide.prmcrd -outname lambda
> > sh: ambpdb: command not found
> > sh: rdparm: command not found
> > Parsing PDB file lambda.pdb...
> > found:
> > 0 protein residues
> > 0 sodium ions
> > 0 chloride ions
> > 0 waters
> >
> > Use of uninitialized value in printf at ./amb2gmx.pl line 263.
> > 0 TOTAL residues read
> > Reading prmtop file...
> > 0 atom type indices read.
> >
> > found:
> > 0 atoms
> > 0 bonds
> > 0 angles
> > 0 torsions
> >
> > Qtot = 0
> > Qmax = 0 at atom -1
> >
> > Constructing list of unique nonbonded atomtypes...
> > 0 unique atomtypes found.
> > Writing atom types...
> > Done.
> >
> > And nothing generates inside top and gro files.
> >
> >
> > Please help me.
> >
> > Madhumita Das
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 14 2011 - 01:00:04 PDT
