[gmx-users] about PRODRG

[Justin A. Lemkul]

fancy2012 wrote:
> Dear GMX users,
>  When I prepare the topology file of one small molecule using PRODRG, I 
> find that the generated topology file is for another molecule. The only 
> difference between the two molecules is that the latter one has one more 
> double bond. How should I deal with such problems? Thanks very much!
>  

That's very odd, but it's simple to correct the affected bonded parameters and 
atom types (if necessary) to reflect the desired molecule.

Also note:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-Justin

> All the best,
> qinghua
>  
> 

-- 
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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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