Dear Amber users,
sorry, I accidently sent unfinished letter previously.
I was trying to add 12-6-4 parameters to Na+ and Cl- ions in the system
containing DNA (bsc1 force field).
The result was
> add12_6_4 .Na+,Cl- watermodel SPCE
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
read from [/home/nick/amber18/dat/leap/parm/lj_1264_pol.dat]. Using default
C4 parameters for water model [SPCE].
***********************************************************
The selected metal ion is Na
The selected metal ion is Cl
Action add12_6_4 failed
LJ12_6_4Error: Could not find parameters for ATOM_TYPE CE
> quit
Then I decided to experiment and added vdW parameter for CE in the
lj_1264_pol.dat:
CE 1.352
and tried again:
> add12_6_4 .Na+,Cl- watermodel SPCE
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
read from [/home/nick/amber18/dat/leap/parm/lj_1264_pol.dat]. Using default
C4 parameters for water model [SPCE].
***********************************************************
The selected metal ion is Na
The selected metal ion is Cl
Action add12_6_4 failed
LJ12_6_4Error: Polarizability parameter of AMBER_ATOM_TYPE
CI is not the same as that of AMBER_ATOM_TYPE CE but their VDW parameters
are the same.
How is it possible to solve the issue with CE parameter and polarizability
and with adding 12-6-4 to the system? For a protein sytem it worked well.
Kind regards,
Nick
Nikolay Kuzmich
Department of Drug Safety,
Research Institute of Influenza,
WHO National Influenza Centre of Russia,
15/17 Professor Popov St.,
Saint-Petersburg
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Received on Mon Oct 08 2018 - 02:30:03 PDT
