Thanks that helped a lot so the nonb for NB from Histidine is the same
as nitrogen?
N 1.8240 0.1700 OPLS
On Wed, Feb 23, 2011 at 2:35 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Feb 23, 2011 at 6:37 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
>
>> 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?
>>
>
> Yes. Amber's polariz(s)able force field is amoeba, so these parameters have
> no meaning outside of that context. You can find the full format
> specification of *most* amber files at http://ambermd.org/formats.html.
>
> This includes the parameter files, prmtop files, etc.
>
> Hope this helps,
> Jason
>
>
>> 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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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Feb 23 2011 - 06:30:06 PST
