Good morning
I work in the setup of a metaloprotein (Cu+2), using the V.15 of AmberTools.
For this system fortunately exist published the Amber parameters. But,
when tleap read:
> loadamberparams *.frcmod
(file that include some of these special parameters), there are 3 that
don't read.
The *.frcmod file has the next information regarding to the bond parameters
ANGLE
V-NB-Cu+2 125.000 10.000
NB-Cu+2-na 109.500 0.010
NB-Cu+2-NB 109.500 0.010
NB-Cu+2-Omu2 109.500 0.010
CR-NB-Cu+2 127.000 10.000
O-C-n2 80.000 122.900
CX-C-n2 70.000 116.600
c-N-H 50.000 118.040
c-N-CX 70.000 116.600
O-C-n2 80.000 122.900
na-Cu+2-NB 109.500 0.010
na-Cu+2-Omu2 109.500 0.01
Cu+2-Omu2-Omu2 70.000 10.000
Cu+2-Omu2-Cu+2 138.000 10.000
Omu2-Cu+2-Omu2 109.500 0.010
cc-na-Cu+2 127.000 10.000
c2-na-Cu+2 125.000 10.000
Cu+2-Omu2-Omu2 70.000 10.000
Cu+2-Omu2-Cu+2 138.000 10.000
Omu2-Cu+2-Omu2 109.500 0.010
This is the output message
--------------------------
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Cu+2 - Omu2 - Cu+2
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Cu+2 - Omu2 - Cu+2
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Cu+2 - Omu2 - Omu2
Could not find angle parameter: Omu2 - Cu+2 - Omu2
Could not find angle parameter: Omu2 - Cu+2 - Omu2
------------------------
Others similar warning message were solved adjusting the order of the
alert with the sequence in which read the parameters in the *.frcmod
file and work, but in this case this solution does not work. I don't
understand what happens, I thought that could be due to the format,
but these parameters are in the same format that the other ones. I
treat to move the parameters to the top of the angle section, but then
tleap don't read the others parameters.
Thanks a lot for any advice and for your time.
Lea Toledo
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Received on Tue Jun 28 2016 - 04:30:02 PDT
