Hello,
I have been following a tutorial outlining the method on how to use
antechamber to assign GAFF parameters and BCC charges to a molecule (
http://ambermd.org/tutorials/basic/tutorial4b/). However, I am having a
hard time rationalizing two of the dihedral parameters selected for my
molecule (acetaminophen). I have two questions
1) broadly speaking, is there anyway to know the list of dihedral pairs
being used. For instance, the prmtop file lists the dihedral force
constants, periodicity, and dihedral phase. However, its not clear to me
from the tutorial, or the amber manual, how to determine what dihedral
pairs those parameters are in reference to. Is there a way to do this, not
only necessarily for the dihedrals, but also for the bonded, and angle
pairs?
2) If 1 cannot be done, could someone help me rationalize the parameters I
received? Here is my acetaminophen pdb file:
ATOM 1 C8 MOL 1 3.537 1.423 -0.000 1.00 0.00
ATOM 2 H7 MOL 1 3.100 1.168 -0.969 1.00 0.00
ATOM 3 H8 MOL 1 2.867 1.109 0.787 1.00 0.00
ATOM 4 H9 MOL 1 3.620 2.496 0.054 1.00 0.00
ATOM 5 C7 MOL 1 4.909 0.795 0.113 1.00 0.00
ATOM 6 O2 MOL 1 5.702 0.876 -0.810 1.00 0.00
ATOM 7 N1 MOL 1 5.186 0.254 1.304 1.00 0.00
ATOM 8 H6 MOL 1 4.433 0.190 1.973 1.00 0.00
ATOM 9 C1 MOL 1 6.371 -0.427 1.713 1.00 0.00
ATOM 10 C2 MOL 1 7.614 -0.239 1.116 1.00 0.00
ATOM 11 H1 MOL 1 7.731 0.455 0.298 1.00 0.00
ATOM 12 C3 MOL 1 8.723 -0.940 1.578 1.00 0.00
ATOM 13 H2 MOL 1 9.682 -0.773 1.121 1.00 0.00
ATOM 14 C4 MOL 1 8.596 -1.832 2.645 1.00 0.00
ATOM 15 O1 MOL 1 9.705 -2.516 3.051 1.00 0.00
ATOM 16 H5 MOL 1 9.593 -2.902 3.943 1.00 0.00
ATOM 17 C5 MOL 1 7.371 -2.006 3.257 1.00 0.00
ATOM 18 H3 MOL 1 7.261 -2.676 4.098 1.00 0.00
ATOM 19 C6 MOL 1 6.255 -1.299 2.796 1.00 0.00
ATOM 20 H4 MOL 1 5.292 -1.448 3.261 1.00 0.00
TER
END
I performed the following steps:
antechamber -i acetaminophen.pdb -fi pdb -o acetaminophen.mol2 -fo mol2 -c
bcc -s 2
parmchk -i acetaminophen.mol2 -f mol2 -o ac.frcmod
source leaprc.gaff
AC = loadmol2 acetaminophen.mol2
check AC
loadamberparams ac.frcmod
saveoff AC ac.lib
saveamberparm AC ac.prmtop ac.inpcrd
My prmtop contains the following values for the dihedrals:
%FLAG
DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.50000000E+00 8.00000000E-01 8.00000000E-02 0.00000000E+00
4.50000000E-01
2.00000000E+00 3.62500000E+00 9.00000000E-01 1.05000000E+01
1.10000000E+00
%FLAG
DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00 1.00000000E+00 3.00000000E+00 2.00000000E+00
2.00000000E+00
1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG
DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
3.14159400E+00
Now, I was doing my due diligence and checking the parameters generated
prior to performing simulations. I cannot for the life of me determine
where that 0.8 kcal/mol and 2.0 kcal/mol force constants (as well as
associated periodicty and phase parms) come from. Could someone help
identify what dihedral pair this is referencing?
Regards,
Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
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Received on Sat Apr 30 2016 - 21:30:02 PDT
