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 - 21:11:46 PDT
