Hi,Thank you so much
Command:
[roja.localhost bin]$ /home/roja/amber17_FIRST/bin/parmed sustiva/script.py
Error;
Traceback (most recent call last):
File "/home/roja/amber17_FIRST/bin/parmed", line 5, in <module>
from parmed.scripts import clapp
ImportError: No module named parmed.scripts
Sent from my iPhone
> On Feb 4, 2018, at 9:25, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Feb 05 2018 - 06:00:05 PST
