what does the ac.frcmod file say under DIHE?
Andrew
On Saturday, April 30, 2016, conor parks <coparks2012.gmail.com> wrote:
> 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 - 22:30:03 PDT
