Dear Senal
The error is generally pdb4amber command. It does not read charge or
occupancy (pqr or pdb) number because number digit is more than in normal
pdb file.
When you just delete the number its work.
I have remove two extra number mentioned below and it really works.
I don't know the reason but it works.
ATOM 1 N SER 4 -12.259 88.217 33.996 0.18
1.5500 N
ATOM 2 H1 SER 4 -12.829 87.385 33.909 0.1811
1.3000 H
ATOM 3 H2 SER 4 -11.412 88.101 33.454 0.1811
1.3000 H
Regards
Aashish Bhatt
On Thu, May 24, 2018 at 5:25 PM, 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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> > 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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>
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Received on Thu May 24 2018 - 06:30:03 PDT
