Hi all again,
Yes, you were absolutely helpful..
Yes, the idea should be to modify the atom types (and not the atom name) in
order to treat the force field for RNA only..
If understand correctly (and hopefully that should be a possible summary
useful for everyone):
-Tleap reads the unit names from pdb file
- It finds the corresponding ones in the lib file
Consequences:
- changing atom charges should not be a “huge” problem
- More caution should be taken when we are “modifying” parameters
corresponding to atom types
Possible strategy specific for our case:
- create 4 prepin files, one for each RNA bases with modified atom types
for those atoms that are touched by the new parameters.
for example adding R at the end:
*i.e.* O2 -> O2R
- create a frcmod files with the new parameters with those “R”-atom types
On Sun, Aug 19, 2018 at 2:01 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Sat, Aug 18, 2018, Antonio Amber Carlesso wrote:
> >
> > A) to create 4 prepin files, one for each RNA bases with modified atom
> > types for those atoms that are touched by the new parameters by, for
> > example adding R at the end: e.g. like H62 -> H62R.
> >
> > B) create a frcmod files with the new parameters with those “***R”-atom
> > types.
>
> I think you are confusing atom *names* with atom *types*. The latter
> are always 2 characters, and are what the force field is based on.
>
> Atom names are specified by the IUPAC and the PDB, and are standards.
> They have nothing to do with what force field is being used. So "H62" is
> an atom name, and should not be changed.
>
> ...hope this helps....dac
>
>
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Received on Sun Aug 19 2018 - 05:00:02 PDT
