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

Jacob Spooner 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:
> 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 :)


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. 

> 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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