Hi,
On Sat, 31 Mar 2007, Carlos Simmerling wrote:
> there is no such thing as ff03 DNA or RNA parameters, at least not yet.
Yes, and this is indicated in the manual.
But if one sources leaprc.ff03 then one can load a dna containing pdb
and save the prmtop.
What is the equivalent procedure for a rna containing pdb ?
Late at night Dave wrote:
> On Sat, Mar 31, 2007, Scott Brozell wrote:
> >
> > I plan to upgrade DOCK's Amber Score from ff94 to ff03.
> > Comments are welcome.
>
> ff99SB is perhaps a better choice, since it's charge model is more like that
> of gaff, which is what dockers will be using for the ligand.
As above where is the rna equivalent ?
thanks,
Scott
> On 3/31/07, Scott Brozell <sbrozell.scripps.edu> wrote:
> > Hi,
> >
> > Why does this file not exist: leaprc.rna.ff03 ?
> >
> > Why is the organization of the leaprc files inconsistent ?
> > One would expect that a diff between dna and rna leaprc pairs
> > would show only dna and rna diffs. Instead there are some
> > curious and irrelevant diffs: diff leaprc*.ff94
> > (what's up with { "EP" "" "sp3" } ? how about consistent comments ?)
> >
> > Missing atom types for ions were finally added in ff03, but why
> > were they missing in ff99, etc ? The comment in ff03 is useless:
> > # things should be there
> >
> >
> > I plan to upgrade DOCK's Amber Score from ff94 to ff03.
> > Comments are welcome.
Received on Wed Apr 04 2007 - 06:07:32 PDT
