Hello Amber：
I performed a metal protein MD by amber. There are four calcium irons in the protein. I followed the tutorials on amber page. when I input this command:
parmed.py -n -O mod_wat.prmtop parmed.in
an error occurs below:
Loaded Amber topology file mod_wat.prmtop
['parmed.in']
Reading actions from parmed.in
Loading restart file mod_wat.inpcrd
Files are overwritable
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities read from [/home/shaox/amber14/dat/leap/parm/lj_1264_pol.dat]. Using default C4 parameters for water model [SPCE].
***********************************************************
The selected metal ion is C
Action add12_6_4 failed
LJ12_6_4Error: Could not find parameters for ATOM_TYPE N3
My protop and inpcrd files have been generated successfully. The parmed.in file is edited below:
loadRestrt mod_wat.inpcrd
setOverwrite True
add12_6_4 :40.CA watermodel SPCE
outparm mod_wat_ca.prmtop mod_wat_ca.inpcrd
Does the number 40 before @CA indicate atomic weight?
How can I solve this problem, please?
yours
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 27 2015 - 22:00:03 PST
