[gmx-users] Not sure how to include dihedral angle params of ATP into force field

Piggot T. 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?

Thank you!
Zheng Ruan
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