[gmx-users] Not sure how to include dihedral angle params of ATP into force field
T.Piggot at soton.ac.uk
Tue Feb 16 12:08:18 CET 2016
I have an itp for ATP that I made a while ago which has these parameters included. I can send it off list if you like?
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Zheng Ruan [zruan1991 at gmail.com]
Sent: 16 February 2016 02:22
To: gmx-users at gromacs.org
Subject: [gmx-users] Not sure how to include dihedral angle params of ATP into force field
Hi Gromacs Users,
I am trying to add ATP molecule into amber99sb-ildn force field by
using the parameters suggested in
(http://www.ncbi.nlm.nih.gov/pubmed/12759902). I known the problem has
been discussed previously, but I still cannot figure out how to
convert the torsion params proposed in the paper into gromacs.
Specifically, there is a table that describes the torsion angle
parameters in the paper:
Torsion No._of_paths(1) Vn/2(2) gamma(3) n(4)
HC-CT-OS-P 3 0.105 0.00 3.0
CT-OS-P-OS 1 -1.560 0.00 1.0
CT-OS-P-O2 2 1.179 0.00 -3.0
CT-OS-P-O2 2 -0.812 0.00 2.0
P-OS-P-OS 1 0.897 0.00 1.0
P-CS-P-O2 2 -0.709 0.00 2.0
P-CS-P-O3 3 -0.255 0.00 3.0
(1) Number of bond paths that the total Vn/2 is divided into.
(2) Magnitude of torsion in kcal/mol.
(3) Phase offset in degrees.
(4) The periodicity of the torsion.
I think the corresponding part in the ff is [dihedraltypes] in
ffbonded.itp, where it looks like this:
[ dihedraltypes ]
;i j k l func phase kd pn
CA CA CA OH 4 180.00 4.60240 2 ; new99
H5 O C OH 4 180.00 4.60240 2 ; new99
H5 O C OS 4 180.00 4.60240 2 ; new99
I'm not quite sure about the exact physics behind these parameters.
But just by looking at the units, Vn/2 corresponds to kd; gamma
correponds to phase; and n relates to pn. What confused me is the
negative number in Vn/2 and n. What kind of unit transformation should
I do to put the params in the param table to ffbonded.itp?
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