[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:
>> 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 :)
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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