On 10/17/2012 08:35 PM, Justin Lemkul wrote:
You need GB parameters for every atom type in the system. Most
protein and nucleic acid types work out of the box, but if you have a
complex system with some novel molecule in it, you have to add
parameters for the atom types that it uses.
thank you for kind reply. But I do add them in my .top file with line:
#include "ligand.itp"
And in the ligand.itp, it contains all the atom type, I am using Amber
FF for the system and the ligand topology was generated by acpype tools.
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01
; 1.68 0.1700
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01
; 1.91 0.1094
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01
; 1.91 0.0860
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01
; 1.66 0.2100
N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01
; 1.82 0.1700
H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02
; 1.39 0.0157
H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02
; 0.60 0.0157
HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02
; 1.46 0.0150
thank you very much
best
Albert
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