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 |
>
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>
>
Received on Sun Mar 16 2008 - 06:07:50 PDT
