Dear madhumita das
at a first and quick look, I would guess your problem is in the
path of AMBERHOME and how you include it in your PATH variable.
Indeed, your amb2gmx is not able to find ambpdb and rdparm.
sh: ambpdb: command not found
sh: rdparm: command not found
Search where the your amber directory is locate.
For example in my computer
>echo $AMBERHOME
>/usr/local/amber11
Export AMBERHOME to the proper variable, include it in your PATH in the
file ~/.profile file, then
>source ~/.profile
and try again...
Hope this help
Ivan
On 09/30/2011 10:31 AM, madhumita das wrote:
> Hi amber users,
>
> I have generated prmtop and inpcrd files for a residue and I want to convert
> it top and gro files needed for gromacs,but whenever I run the command
> ./amb2gmx.pl -prmtop peptide.prmtop -crd peptide.prmcrd -outname lambda
> following error comes
> ambpdb: command not found
> rdparm: command not found
> Parsing PDB file lambda.pdb...
> found:
> 0 protein residues
> 0 sodium ions
> 0 chloride ions
> 0 waters
>
> Use of uninitialized value in printf at ./amb2gmx.pl line 263.
> 0 TOTAL residues read
> Reading prmtop file...
> 0 atom type indices read.
>
> found:
> 0 atoms
> 0 bonds
> 0 angles
> 0 torsions
>
> Qtot = 0
> Qmax = 0 at atom -1
>
> Constructing list of unique nonbonded atomtypes...
> 0 unique atomtypes found.
> Writing atom types...
> Done.
> sh-3.1# export AMBERHOME=/root/Desktop/SEEMA_YADAV/amber11sh-3.1# export
> PATH=$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
--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.gladich.uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 30 2011 - 03:30:03 PDT
