Hi Ilyas,
thanks for your detailed reply!
So far I have one remark:
> I have checked out the ff03 parameters. The parameters for your system are
> defined in frcmod.ff03 and parm99.dat. Here are the parameters:
> - parm99.dat -
> CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
> CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94
> ---------------
> - frcmod.ff03 -
> CT-CT-C -N 1 0.0560 0.00 -3.
> CT-CT-C -N 1 0.0657 180.00 -2.
> CT-CT-C -N 1 0.7784 180.00 1.
>
> H0-CT-C -N 1 0.0110 0.00 -2.
> H0-CT-C -N 1 1.0607 180.00 1.
> ---------------
> First the parm99.dat is loaded and then the frcmod.ff03 is loaded. As far
> as I see, there are 5 torsional parameter defined for CT-CT-C -N. That
> means that if you do a perturbation from CT-CT-C -N --> H0-CT-C -N, you
> need to defined 5 torsional parameter for H0-CT-C -N, too. (If I am wrong,
> please someone correct me)
My understanding is that loading of the frcmod file with new parameters
for the CT-CT-C -N torsion will OVERWRITE the existing parameters. So,
after reading the frcmod file, 3 parameters are associated with this
torsion...
This is also the reason why I do not understand that leap asks for the
redifinition of torsion parameters that are already loaded.
Thanks again,
Oliver
--
________________________________________________________________
Oliver Hucke, Dr.
Biomolecular Structure Center Health Sciences Building - K418C
Dept. of Biochemistry 1959 NE Pacific St.
University of Washington phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email: ohucke.u.washington.edu
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Received on Wed Jul 13 2005 - 01:53:00 PDT
