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 Sep 30 2011 - 02:00:03 PDT
