[gmx-users] OPLSAA parameters

[friendli]

Thank you Justin.

Can you tell me how i can find the link between atom names and atom types?
The thing I wanna do is to figure out the bond parameters(b0,bk), and so 
the angle, dihedral parameters in oplsaa FF.
Is it possible to give me some examples, such as the bond between CG and 
OG1 in [ASN] in ffoplsaa.rtp?

thanks

Qiang

Justin A. Lemkul wrote:
>
>
> friendli wrote:
>> Dear all,
>>
>> To understand the exact parameters used in oplsaa force field, I read 
>> the ffoplsaa*.*** files.
>> But I can not find all the corresponding atom types in the 
>> ffoplsaa.rtp and ffoplsaabon.itp files.
>>
>> for example, in rtp file, there is a bond between atom type CG and 
>> OG1. But in *bon.itp, there is no such atom types CG or OG1 in the 
>> [bondtypes]. where is the bond constants etc kept? and how Gromacs 
>> find them?
>>
>
> CG and OG1 are atom names, not atom types.  The force field can 
> determine bonds based on atom types.  As long as they are recognized 
> atom types and parameters for such a bond are present, there will be 
> no problem.
>
> -Justin
>
>> Can anybody give a hint for this?
>>
>>
>> thanks in advance
>>
>> Qiang
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>