So it looks like it is a polarization factor - from the tutorial by
Ross Walker on parametrizing a novel residue he omits any value here
so for ordinary MD simulation the polarization effects are omitted?
On Wed, Feb 23, 2011 at 8:14 AM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> Hi all,
>
> I have parametrized a new residue and needed to change the naming of
> some of the atoms in the lib file so I am add the missing parameters.
> I am not quite sure where to find the "nonbonding" interaction terms.
> The residue I am trying to parametrize is a modified water molecule
> and in the parm99.dat file I find the following parameters for TIP3P
>
> MOD4 RE
> .......
>
> OW 1.7683 0.1520 TIP3P water model
> HW 0.0000 0.0000 TIP3P water model
>
> What is the MOD4 and RE section?
>
> The first part second column
>
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
> C 12.01 0.616 ! sp2 C carbonyl group
> CA 12.01 0.360 sp2 C pure aromatic (benzene)
>
> what does the second column mean?
>
>
> Thanks,
>
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Received on Wed Feb 23 2011 - 04:00:04 PST
