On 10/17/12 2:41 PM, Albert wrote:
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
Here you're adding atom types, not the associated GB parameters. Some of these
atom types probably already exist within the gbsa.itp file of the force field,
judging by their names. At least one (OS) does not.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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