So what does "idiv" stands for (sorry I did not find this in manual)?
Why not just use pk/idiv as the pk value in amber ff?
Thanks,
Yun
On Mon, Jul 16, 2012 at 11:31 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Jul 16, 2012, Yun Shi wrote:
> >
> > As a test, I used tleap to save .prmtop and .inpcrd files for RU3
> (R-URACIL
> > - with 5' - phosphate group and 3' - OH group) based on ff99SB.
> >
> > When I inspect the resulting .prmtop file with rdparm, I found the P
> > -O5'-C5'-H5'1 and P -O5'-C5'-C4' dihedral parameters were
> >
> > 0.383 0.00 3.0
> >
> > But these two dihedrals have atom types as P -OS-CT-H1 and P -OS-CT-CT,
> > which should match X -CT-OS-X (1.15 0.0 3.0) in parm99.dat.
>
> They *do* match: the "X -CT-OS-X" line in parm99.dat is this:
>
> X -CT-OS-X 3 1.15 0.0 3.
>
> You have to divide the 1.15 by 3 (the "idiv" value) to get the 0.383 value
> that rdparm reports.
>
> > this 0.383 force constant is from one term of a combination like
> > CT-CT-OS-CT/C/N* (0.383 0.0 -3.0) in parm99.dat.
>
> This is also consistent: the idiv value for CT-CT-OS-CT is 1, so pk/idiv is
> the same as for the generic (wild-card) torsion.
>
> >
> > I also found similar discrepancy for O1P-P -O5'-C5' (atom type: O2-P
> > -OS-CT), which was recognized as only the first term of OS/OH-P -OS-CT
> > (0.25 0.0 -3.0) in the prmtop file. But I assume it should use X -OS-P
> -X
> > (0.75 0.0 3.0).
>
> Same explanation as above: don't ignore the idiv values.
>
> ....dac
>
>
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Received on Mon Jul 16 2012 - 13:30:02 PDT
