Re: [AMBER] Puzzles about calculating binding energy using MMGBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 19 Dec 2013 17:18:42 -0500

Please keep responses posted to the mailing list.


On Wed, Dec 18, 2013 at 9:32 PM, Yanyan ZHU <zhuyanzily.gmail.com> wrote:

> Hi Jason Swails:
>
> Firstly, thank you for your kindhearted.
>
> We have tried using the MMGBSA.py as you mentioned, instead of the
> MMGBSA.pl, however the energy of each residue canít be successfully
> calculated too. And the error is identical in two conditions, as following:*
> bad atom type : hn.* The meaning of hn is a hydrogen atom binding with
> the atom of nitrogen in the structure of ligand.
>

This error occurs in mdread.F90 (or mdread.f) inside $AMBERHOME/src/sander.
 If you search for that string, you should see it in 3 places (but only the
first 2 will print out exactly what you saw). One of them should be
commented out. You can modify the source code to add support for the
missing atom types to eliminate this message (you have to recompile after
doing this).

However, this error should not be occurring if you are using Amber 12,
since parameter determination is done based on atomic number comparisons
rather than atom type name comparisons. If you cannot upgrade to Amber 12,
you will have to modify the source code of sander in order to fix this
problem.

Good luck,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 19 2013 - 14:30:03 PST
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