Hej,
Just use acpype Paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461484/
Download here
https://github.com/t-/acpype
Usage:
acpype -p com_solvated.top -x com_solvated.crd -b complex
Acpype can’t make a Gromacs compatible .top file with TIP4P water model
hence we need to add some parts in the complex_GMX.top file to make it
Gromacs compatible.
In that case please see section 7 (*Manipulate the topology file*) of
https://cbiores.com/from-docking-to-dynamics/
Good Luck,
/SB
On Mon, Feb 5, 2018 at 2:55 PM, Roja <roja.rhmn.gmail.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
Doctoral Student, Division of Biophysical Chemistry, CMPS, Lund University,
Sweden
Webpage: http://www.cmps.lu.se/bpc/people/soumendranath-bhakat/
Homepage: https://cbiores.com/ <https://cbiores.wordpress.com/>
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
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Received on Mon Feb 05 2018 - 06:30:07 PST
