Re: [AMBER] Error in using pdb4amber command

From: senal dinuka <senal.ichemc.edu.lk>
Date: Thu, 24 May 2018 17:25:14 +0530

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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>



-- 
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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Received on Thu May 24 2018 - 05:00:08 PDT
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