Hi Jason,
I found the issue.
At the time of porting, the implementation has been validated against
AMBER 8 and the results have matched very precisely the GROMACS ones.
Looking at the sources, AMBER 8 has in amber8/dat/leap/cmd/leaprc.ff03:
..snip..
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
..snip..
This has been updated in later Amber versions. E.g. in the latest AMBER
14 amber14/dat/leap/cmd/leaprc.ff03.r1 has:
..snip..
loadOff all_aminoct03.lib
loadOff all_aminont03.lib
..snip..
I will update those in Gromacs too.
Cheers,
Rossen
On 15/05/14 17:30, Jason Swails wrote:
> On Thu, 2014-05-15 at 16:05 +0200, Rossen Apostolov wrote:
>> Hi,
>>
>> The NALA terminal charges are the same in both Amber03 and Amber99
> This is not true. From the Amber distribution:
>
> NALA in FF03 (last column is charge):
>
> "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
>
> NALA in FF94/FF99/FF99SB/FF12SB (last column is charge):
>
> "HH31" "HC" 0 1 131072 1 1 0.112300
> "CH3" "CT" 0 1 131072 2 6 -0.366200
> "HH32" "HC" 0 1 131072 3 1 0.112300
> "HH33" "HC" 0 1 131072 4 1 0.112300
> "C" "C" 0 1 131072 5 6 0.597200
> "O" "O" 0 1 131072 6 8 -0.567900
>
> Likewise for the C-terminal residues, the charges are different.
>
>> although the corresponding ALA residue charges are different in those
>> forcefields. Here is the report by a Gromacs user who noticed it:
>> http://redmine.gromacs.org/issues/1466
> The person that reported the problem in that file pointed out that the
> charges are the same in the _Gromacs_ files but that they are not the
> same in the _Amber_ files.
>
>> Is that correct or the charges need to be fixed?
> The Gromacs files need to be fixed in order to run ff03 with proper
> termini.
>
> Hope this helps,
> Jason
>
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Received on Wed May 21 2014 - 07:30:05 PDT
