ah, that makes more sense then. this seems like a great improvement,
but I think there should be a way to denote the changed version since
users and readers of articles will want a way to clearly differentiate
between work done using the "original" and "bugfix" ff03. otherwise
work with "ff03" won't be reproducible.
On Mon, Mar 17, 2008 at 4:03 PM, Ray Luo <rluo.uci.edu> wrote:
> Clarification: these charges were derived using the strategy, not the
> charging scheme, with which the ff94 nt/ct charges were derived ... if you
> did this before you know what I meant ... Of course the derivation was based
> on the same ESP from b3lyp/cc-pvtz as ff03.
> Best,
> Ray
>
> On Mar 17, 2008, at 11:52 AM, Carlos Simmerling wrote:
>
> this seems inconsistent- if they are ff94 charging scheme, how are they
> ff03 files? I think this is going to be very confusing to users.
>
> On Mon, Mar 17, 2008 at 2:20 PM, Ray Luo <rluo.uci.edu> wrote:
>
> > Hi Yong and Ross,
> >
> > I forgot to mention that we developed a set of ff03aa nt/ct prepin
> > files according to the ff94 charging scheme for the terminal
> > residues. If you want to put it into amber10, I can email you the file.
> >
> > All the best,
> > Ray
> >
> > On Mar 14, 2008, at 11:20 PM, Yong Duan wrote:
> >
> > >
> > > Yes, I would think we need to update the lib files in AMBER 10 and
> > > release a
> > > patch for AMBER 9.
> > >
> > > Leap ignores ACE in all_amin03.lib? Really? Hmmm ....
> > >
> > > For proteins of the charged terminal groups, the nt and ct versions
> > > of ff94
> > > charges are used.
> > >
> > > yong
> > >
> > > -----Original Message-----
> > > From: owner-amber-developers.scripps.edu
> > > [mailto:owner-amber-developers.scripps.edu] On Behalf Of Ross Walker
> > > Sent: Friday, March 14, 2008 9:09 PM
> > > To: amber-developers.scripps.edu
> > > Subject: RE: amber-developers: FF03 Charge problems in lib files?
> > >
> > >
> > > Hi Yong,
> > >
> > > Should we update the lib file for ACE and PRO for the AMBER 10
> > > release?
> > > Release a patch for AMBER 9?
> > >
> > > Also, what about the issue with the ACE in all_amino03.lib being
> > > ignored by
> > > leap? And the nt and ct versions using FF94 charges?
> > >
> > > All the best
> > > Ross
> > >
> > >> -----Original Message-----
> > >> From: owner-amber-developers.scripps.edu
> > >> [mailto:owner-amber-developers.scripps.edu] On Behalf Of Yong Duan
> > >> Sent: Friday, March 14, 2008 11:49
> > >> To: amber-developers.scripps.edu
> > >> Subject: RE: amber-developers: FF03 Charge problems in lib files?
> > >>
> > >>
> > >> Hi, Ross,
> > >>
> > >> Thanks for pointing that out. Yes, indeed. For some reason,
> > >> the round-up
> > >> error made the difference. I should have checked this. Here
> > >> is the modified
> > >> version.
> > >>
> > >> "HH31" "HC" 0 1 131072 1 1 0.076010
> > >> "CH3" "CT" 0 1 131072 2 6 -0.190263
> > >> "HH32" "HC" 0 1 131072 3 1 0.076010
> > >> "HH33" "HC" 0 1 131072 4 1 0.076010
> > >> "C" "C" 0 1 131072 5 6 0.512403
> > >> "O" "O" 0 1 131072 6 8 -0.550170
> > >>
> > >> Thanks!
> > >>
> > >> yong
> > >>
> > >> -----Original Message-----
> > >> From: owner-amber-developers.scripps.edu
> > >> [mailto:owner-amber-developers.scripps.edu] On Behalf Of Ross Walker
> > >> Sent: Friday, March 14, 2008 10:09 AM
> > >> To: amber-developers.scripps.edu
> > >> Subject: amber-developers: FF03 Charge problems in lib files?
> > >>
> > >>
> > >> Hi All,
> > >>
> > >> This was initially brought to my attention by Brent Gregerson
> > >> at D.E. Shaw
> > >> but upon further digging I find that there appear to be more
> > >> complex issues
> > >> that I am wondering if anyone can comment on.
> > >>
> > >> If we look at the definition of ACE in all_amino03.lib we have:
> > >>
> > >> !entry.ACE.unit.atoms table str name str type int typex
> > >> int resx int
> > >> flags
> > >> int seq int elmnt dbl chg
> > >> "HH31" "HC" 0 1 131072 1 1 0.076010
> > >> "CH3" "CT" 0 1 131072 2 6 -0.190264
> > >> "HH32" "HC" 0 1 131072 3 1 0.076011
> > >> "HH33" "HC" 0 1 131072 4 1 0.076010
> > >> "C" "C" 0 1 131072 5 6 0.512403
> > >> "O" "O" 0 1 131072 6 8 -0.550170
> > >>
> > >> Note the extra +0.000001 of charge on HH32. I agree that this
> > >> is somewhat
> > >> just lost in the noise but it is strange that the extra
> > >> charge required to
> > >> neutralize the residue was added to a 'supposedly' degenerate
> > >> hydrogen and
> > >> not to the central carbon. What was the reasoning behind
> > >> this? While it
> > >> likely does not end up giving statistically significant
> > >> differences in
> > >> results it of course makes certain optimizations (which could
> > >> exploit the
> > >> degeneracy in the hydrogens) impossible without changing things.
> > >>
> > >> I should point out that the same situation occurs for HD2 in PRO.
> > >>
> > >> However, when I dug deeper into this I was at first surprised
> > >> to find that
> > >> ACE is in the all_amino03.lib file since it is a c-terminal
> > >> residue. Thus it
> > >> should be in all_aminoct03.lib. Only this file does not
> > >> exist. Instead the
> > >> leaprc.ff03 file loads all_aminoct94.lib, then all_aminont94.lib then
> > >> all_amino03.lib.
> > >>
> > >> ACE is defined in both all_aminoct94.lib and all_amino03.lib.
> > >> Since the ct94
> > >> is loaded first leap uses the charges in here for the ACE
> > >> residue. Hence you
> > >> get the HF/6-31G* charges from the original Cornell et al
> > >> JACS paper. Thus
> > >> the charges mentioned above for ACE are never used. (However,
> > >> the PRO issue
> > >> still remains).
> > >>
> > >> More of a concern though is that as far as I can tell this
> > >> means that while
> > >> all regular residues would use the FF03 charge model any C or
> > >> N termini will
> > >> use the Cornell et al charges. This would seem to be somewhat
> > >> inconsistant
> > >> and I was wondering if anyone can explain this.
> > >>
> > >> Comments?
> > >>
> > >> All the best
> > >> Ross
> > >>
> > >> /\
> > >> \/
> > >> |\oss Walker
> > >>
> > >> | Assistant Research Professor |
> > >> | San Diego Supercomputer Center |
> > >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > >> | http://www.rosswalker.co.uk | PGP Key available on request |
> > >>
> > >> Note: Electronic Mail is not secure, has no guarantee of
> > >> delivery, may not
> > >> be read every day, and should not be used for urgent or
> > >> sensitive issues.
> > >>
> > >>
> > >
> >
> >
>
>
Received on Fri Apr 18 2008 - 21:11:49 PDT
