you would need to tell people how you generated the prmtop- what program,
what version what is the molecule(s) involved, and so on.
On Fri, Oct 12, 2012 at 5:23 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> ---------- Forwarded message ----------
> From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
> Date: Fri, Oct 12, 2012 at 2:24 PM
> Subject: Notes and warnings in the generalized Born calculation
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Hi all,
>
> I go the following notes and warnings in the output files (mdout) for the
> generalized Born MD calculations.
>
> Note: 1-4 EEL scale factors were NOT found in the topology file.
> | Using default value of 1.2.
>
> I need a suggestion on how to have those 1-4 EEL scale factors in the
> .prmtop file. Would it have a big effect if I leave it as it is (with
> default value of 1.2)?
>
> | Note: 1-4 VDW scale factors were NOT found in the topology file.
> | Using default value of 2.0.
>
> I need a suggestion on how to have those 1-4 VDW scale factors in the
> .prmtop file. Would it have a big effect if I leave it as it is (with
> default value of 2.0)?
>
>
> | WARNING: ATOMIC_NUMBER section not found. Guessing atomic numbers from
> | masses for GB parameters. Remake topology file with AmberTools
> 12+
> | or add atomic numbers with ParmEd to remove this warning.
>
> Here, I would really appreciate a suggestion on how to add atomic numbers
> using ParmEd.
>
> Thank you
>
> Sajeewa Dewage
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>
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Received on Fri Oct 12 2012 - 14:30:03 PDT
