[gmx-users] How to edit the cgnr and charge fields of a ITP file with the result of Gaussian?

[Justin A. Lemkul]

Liao Chuan wrote:

<snip>

> 
> Then it comes to edit the ITP file. But there are some problems puzzling me.
> 
> Firstly, the ITP file just has 9 atoms ( see above) as the Dundee PRODRG 
> server uses united-atom force field which neglects 5 unpolar hydrogen 
> atoms while the result of Gaussian has 14 atoms. How should I edit the 
> charges of ITP file? Or how could I edit the cgnr and charge fields of 
> the ITP file with the Gaussian result? Is it reasonable and acceptable 
> that a charge group has a decimal number of charges?
> 
> Secondly, the charge group number of ITP file is 3 whereas the result of 
> Gaussian has only one charge group(14 atoms as a whole group). Could the 
> Gaussian package calculate the charges of a molecules by first dividing 
> the atoms of the molecule into different charge groups?
> 
> Any help/suggestions will be greatly appreciated!
> 
>  

Quantum calculations are usually unnecessary for parameterizing molecules under 
Gromos.  In fact, no quantum calculations were done in the original charge 
assignment for the force fields, so one could argue that QM is actually the 
wrong way to do things.

I have found that functional groups are reasonably transferable between 
different molecules, i.e. you could take the charges from a SER sidechain, 
making each alcohol on glycerol a charge group, and you'd probably have a 
reasonable starting point.

Of course, the standard advice follows that a demonstration that these charges 
are appropriate is necessary, following the methodology prescribed in the 
original force field derivation.  For Gromos, this involves reproducing various 
liquid-state thermodynamic properties.

-Justin

> 
> Thank you!!
> 
> Chuan Liao
> 
>  
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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