[gmx-users] How to run solvation dynamics for some organic molecules

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> Dear all,
>              I have generated .gro and .top file for Chloranil from 
> prodrg  and tried solvate it using pre-equilibrated cyclohexane. When i 
> tried to generate the box containing solute it is not modifying the .top 
> file and it shows zero solvent.
> Please help me how to solvate organic molecules that are obtainde from 
> prodrg.
> 

genbox only adds SOL entries, nothing else.  Modify the topology by hand. 
Hopefully you have already done a proper parameterization, as the results from 
PRODRG are likely to be quite inaccurate:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

-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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