[gmx-users] Acetonitrile with CHARMM ff

Justin Lemkul jalemkul at vt.edu
Thu Jul 6 14:27:57 CEST 2017

On 7/6/17 6:34 AM, Sonia Milena Aguilera Segura wrote:
> Dear Justin,
> Thank you for your reply. I went trough the CHARMM forum and I found this post of 2007,
> https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=28545, which basically underlines the same issues I am having. I read this post before posting here, and this why I came with the idea of modifying the dihedral ff parameters, as suggested in the forum. Apparently, it may work if I set the amplitude k=0 and I distort the linear angle a little (maybe 179.9) in the initial structure. The thing is, as I say before, I have no experience modifying force fields, so I wouldn't what to put and where. My guess is that I would need to go the ffbonded.itp file and modify and add the following lines in this way:
> [ angletypes ]
> ;      i        j        k  func       theta0       ktheta          ub0          kub
> CG331    CG1N1    NG1T1     5   179.900000   177.401600   0.00000000         0.00
> [ dihedraltypes ]
> ;      i        j        k        l  func         phi0         kphi  mult
>       HGA3     CG331    CG1N1  NG1T1     9     0.000000     0.000000     1
> [ dihedraltypes ]
> ; 'improper' dihedrals
> ;      i        j        k        l  func         phi0         kphi
>       HGA3     CG331    CG1N1  NG1T1     9     0.000000     0.000000     1
> Please let me know if this makes any sense. Is it correct to modify the angletype or should I only modify the initial structure?

You can modify the [angletype] parameters.  A simple energy minimization will 
correct the structure.  With respect to the dihedrals, as noted in that link, 
they simply shouldn't be there.  You can do as above with a k=0 parameter (don't 
add an improper, though harmless in this case it is incorrect to add these terms 
to methyl groups).  Or, if you want to avoid adding dummy parameters, just 
remove the dihedral lines from your .top file altogether.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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