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 - 21:11:47 PDT
