I don't think that script is actively maintained anymore.
You can use ParmEd to do this. Write a Python script with the following
contents:
import parmed as pmd
parm = pmd.load_file('sustiva.prmtop', 'sustiva.inpcrd')
parm.save('sustiva.top', format=gromacs)
parm.save('sustiva.gro')
Then execute that file (let's say you called it 'script.py') like so:
amber.python script.py
HTH,
Jason
On Sat, Feb 3, 2018 at 2:15 AM, roja rahmani <roja.rhmn.gmail.com> wrote:
> Hi,i'm beginner. i use AMBERtools17, and i want to convert .prmtop and
> .incprd files to GROMACS topology files.i use this script
> https://github.com/choderalab/mmtools/blob/master/converters/amb2gmx.pl
>
> >> perl amb2gmx.pl --prmtop sustiva.prmtop --crd sustiva.inpcrd --outname
> sustiva
> and i get this error;
>
> sh: ambpdb: command not found
> sh: rdparm: command not found
> Parsing PDB file sustiva.pdb...
> found:
> 0 protein or solute residues
> 0 sodium ions
> 0 chloride ions
> 0 magnesium ions
> 0 waters
>
> 0 TOTAL residues read
> Reading coordinates from CRD file...Reading prmtop file...
> 0 atom type indices read.
>
> found:
> 0 atoms
> 0 bonds
> 0 angles
> 0 torsions
> BAD BOX OR BOX NOT DETECTED; USING DUMMY BOX SIZE IN GRO FILEBAD BOX OR BOX
> NOT DETECTED; USING DUMMY BOX SIZE IN GRO FILE
> Qtot = 0
> Qmax = 0 at atom -1
>
> Constructing list of unique nonbonded atomtypes...
> 0 unique atomtypes found.
> Writing atom types...
> Done.
> would you please help me?
>
> Thank you
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Sat Feb 03 2018 - 22:00:01 PST
