[gmx-users] OPLS AA simulation of beta-lactam system

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 19 01:51:59 CET 2010

Jacob Spooner wrote:
>>>> "Justin A. Lemkul" <jalemkul at vt.edu> 1/18/2010 3:23 PM >>>
> Jacob Spooner wrote:
>> Hello,
>> I am planning to run some free energy of solvation calculations on a 
>> drug/enzyme system.  I want to start out with pen-G as my drug.  I have
>> found that OPLS atoms 685-687 describe the beta-lactam portion of my drug,
>> but I see that they are left out of the gromacs ffopls**.itp/atp files.  Is
>> this because there is a problem with implementing these parameters within
>> GROMACS ?  Any help on this topic would be greatly appreciated.
> In principle, no.  If you have parameters for a certain species you can 
> certainly implement them.  You've even identified the files that would need
> to be modified to accommodate your new atom types :)
> -Justin
> Thanks Justin!
> Maybe implemented wasn't the best choice of word, because I am aware that I
> am able implement parameters that I have produced which are not included in
> my chosen force field.  I was more wondering if there is a reason why the
> opls list included in GROMACS skips these numbers.

I think this is something that has been reported before - some small subset of 
atom types are not present in the force field parameter files.  You could always 
submit a bugzilla with the fixed files, requesting that they be implemented in 
the future.  Probably just a consequence of continued force field development, 
something gets left out over time.


>> Thanks Jake Spooner


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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