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
>
>
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Received on Fri Oct 14 2011 - 01:00:03 PDT
