Hi Ilyas,
Indeed, you are correct, I believe.... I never spent the time to fully check
this, I have always just added the extra dihedrals with the 0.0 term in them
to be sure.
All the best
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Ilyas Yildirim
> Sent: Thursday, August 28, 2008 2:58 PM
> To: amber.scripps.edu
> Subject: RE: AMBER: to understand how frcmod.ff99SB works
>
> > Amber allows multiple dihedrals but only if the periodicity is different
> for each dihedral. So in the case below the -4 and -3 periodicity entries
> are added as additional dihedrals while the -2 and 1 entries in
> frcmod.ff99SB should overwrite the existing two entries from parm99.dat.
> >
> > Loading any additional parameters with the same atom types and matching
> periodicities will overwrite existing entries already loaded that match
> that atom type set and periodicity. Hence why FF99SB has
> >
> > C -N -CT-C 1 0.00 0.0 1.
> >
> > This is equivalent of deleting the original 0.8 barrier height dihedral
> from parm99.dat.
> >
> > I hope this helps,
> >
> > Ross
>
> Ross, I thought the way frcmod works is as follows: If you define any
> dihedrals in the frcmod file, it will first remove all the entries from
> the previously defined force field and add the new entries to leap. Let's
> say that my xleap commands are like this:
>
> ---- xleap.in -----
> source leaprc.rna.ff99
> loadamberparams frcmod
> -------------------
>
> and let's say my frcmod file is as follows:
>
> ----- frcmod -----
> Modified dihedral parameters
> MASS
>
> BOND
>
> ANGL
>
> DIHE
> OS-CT-N*-CK 1 5.00 000.0 2. parm98,
> IMPR
>
> NONB
> ------------------
>
> What this will do is, it will remove any entries defined for OS-CT-N*-CK
> and only add this particular dihedral parameter. This means that in the
> prmtop file, there will be only 1 parameter set defined for this
> particular dihedral. In the amber99.dat file, there are 2 sets defined for
> this particular dihedral (2 periodicities).
>
> OS-CT-N*-CK 1 0.00 000.0 -2. parm98,
> OS-CT-N*-CK 1 2.50 0.0 1. parm98,
>
> So, having the above frcmod file will remove the above entries and add
> parameters for the periodicity n=2 only. I just double checked this
> using rdparm. So, I dont think that there is any reason to define zero
> parameters for the unwanted entries (except that if someone is doing TI
> calculation and have this particular entry nonzero).
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Physics - =
> = University of Rochester - =
> = 585-275-6766 (office) - 585-267-5644 (home) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Aug 31 2008 - 06:07:55 PDT
