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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 15 2014 - 09:00:03 PDT
