Hi Senal,
Can you try to edit the below file:
AmberTools/src/pdb4amber/pdb4amber/pdb4amber.py
Change line 506 from
except parmed.exceptions.FormatNotFound:
to
except (parmed.exceptions.FormatNotFound, IndexError):
And "cd $AMBERHOME && make install" to rebuild the pdb4amber.
Let us know if that helps your case.
cheers.
PS: .Dave: In this case, pdb4amber needs to let parmed use "read_PDB"
directly rather the magic "load_file".
Hai
On Thu, May 24, 2018 at 7:55 AM, senal dinuka <senal.ichemc.edu.lk> wrote:
> I have attached here the H++ output (no solvation was carried out).
> Original crystal structure was used as it is as an input while output from
> H++ was used as it is for pdb4amber.
>
> Regards,
>
> On Thu, May 24, 2018 at 5:19 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Thu, May 24, 2018, senal dinuka wrote:
> >
> > > I am using Amber 16 along with Amber Tools 18 version. I was able to
> > > successfully perform pdb4amber command on original crystal structure
> > > (1GQR). But after protonation via H++ server and resubmitting for
> > pdb4amber
> > > following error occurs.
> >
> > Can you send the pdb file (after H++) that is giving the problem?
> > pdb4amber (and the parmed code it is based on) can be rather particular
> > about wanting a correct PDB format. It might also be some problem
> > in our codes that is exposed by having H++ create the input.
> >
> > In either case, we need an example to try to reproduce the problem.
> >
> > ...thx...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> D L Senal Dinuka
> Grad.Chem., A.I.Chem.C.
> Research Assistant
> College of Chemical Sciences
> Institute of Chemistry Ceylon
> Rajagiriya
> Sri Lanka
> +94 77 627 4678
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Sat Jun 02 2018 - 21:00:02 PDT
