You can use 'rdparm' to see if dihedral parameters are correct in your
topology file. After you build the topology file, load the file in rdparm.
Then, try 'printdihedrals'.
On Tue, Mar 16, 2010 at 11:19 AM, Lekpa Duukori <duukori.gmail.com> wrote:
> Hi Everyone,
>
> I have a question about how extra dihedrals are applied.
>
> My study involves a situation where I need to apply an extra N-CT-CT-AO
> dihedral ( AO being a new atom type ).
>
> I make a frcmod file as follows
>
> N -CT-CT-AO 1 0.156 0.0 -3.
> N -CT-CT-AO 1 2.839 0.0 2
>
> with the first line being the original generic X-CT-CT-X included in the
> AMBER .dat files.
>
> My question is: does AMBER still apply this X-CT-CT-X term to my dihedral
> as
> that would be double counting?
>
> Another option would be to edit the parmset in xleap and add only the new
> V2
> dihedral but I am not sure if it also applies the generic one in this case
> as in the parmset X-CT-CT-X does not have the negation on PN.
>
> Thanks.
>
> Lekpa
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>
--
Best,
InSuk Joung
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Received on Tue Mar 16 2010 - 18:30:04 PDT
