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
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sun Mar 16 2008 - 06:07:43 PDT
