[gmx-users] Re: pdb2gmx command

[Justin A. Lemkul]

bharat gupta wrote:
> Sir ,
> 
> I have read both the files description but to create such files I need
> all the bond angles , dihedral angles , connectivity but I don't know
> from where I can get such informations about my molecule ..
> 

Hence why parameterization of novel species is considered an advanced topic. 
Some of these bonded parameters may be adequately assigned by analogy to other 
similar compounds, but in other cases, you have to do a lot of work to derive 
new parameters, and of course, validate them in a manner consistent with the 
original force field.

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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