On Fri, Oct 12, 2012 at 8:24 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> 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)?
>
If you have sugar groups (or anything parametrized with GLYCAM), you will
need to regenerate your prmtop with tleap from AmberTools 12. Otherwise,
this is the correct default.
>
> | 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)?
>
Same answer as above. 2.0 is the 'correct' value for the Amber force
fields.
>
>
> | 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.
>
Open your prmtop in xparmed.py. Click "addAtomicNumber". Click "yes".
Click "Write new prmtop".
Unless you modified the atomic masses in your prmtop, though, this is
unnecessary.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 12 2012 - 17:30:03 PDT
