David, thank you for your response. I'm using the parameters that were
referenced earlier in the thread, from the Bryce group. That is a good
caution; I just assume the improper should be there and was inadvertently
left out. I looked at the thymine residue and it has an improper defined
in the same position, so I feel good about adding it. Thanks again.
Sid
On Fri, Mar 28, 2014 at 1:44 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Mar 28, 2014, Sidney Elmer wrote:
>
> > tleap fails to include an improper torsion term for the new methyl group
> in
> > the DMC residue, i.e.
> >
> > C7 C4
> > \ /
> > C5
> > |
> > C6
> >
> > C6,C4,C5,C7
> >
> > when writing out the prmtop file. Can anyone help me figure out how best
> > to add this term? Thank you in advance.
>
> LEaP looks at the atom types for C6,C4,C5,C7, and adds an improper torsion
> if there is an improper entry in the parameter file that matches those
> types.
> So, you need to see what entries are in your parm.dat file, and add an
> improper entry if you feel that one is needed.
>
> (Are you using the DMC parameters from the Sponer group, as found on the
> contributed parameters database? If so, be sure you want to make changes
> before just adding impropers.)
>
> ....dac
>
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Received on Fri Mar 28 2014 - 15:30:02 PDT
