[gmx-users] about PRODRG

Justin A. Lemkul jalemkul at vt.edu
Tue May 25 13:32:54 CEST 2010

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:



> All the best,
> qinghua


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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