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
--
==================================================
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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