[gmx-users] some question about REMD

[Albert]

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