[gmx-users] OPLS AA simulation of beta-lactam system
Jacob.Spooner at ufv.ca
Tue Jan 19 01:46:02 CET 2010
>>> "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 :)
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.
> Thanks Jake Spooner
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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