[gmx-users] some question about REMD

[Justin Lemkul]

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

-- 
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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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