atom types are in the IAC() array, so if you know which atom numbers are
protein and which are water oxygen, you can directly index the CN1 and CN2
elements using the info shown in that section I quoted before.
On Fri, Jan 6, 2017 at 4:25 PM, Jonathan Huihui <Jonathan.Huihui.du.edu>
wrote:
> So if I wanted to modify those numbers, how would I find out which i,j
> pair represents only a protein-water oxygen interaction?
>
>
> Jonathan Huihui
>
> Graduate Student, University of Denver
>
> Department of Physics & Astronomy
>
> http://portfolio.du.edu/jhuihui2
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, January 6, 2017 2:22:47 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Force field modifications
>
> I think this is the section that you want. All of the pair coefficients are
> pre-calculated in the prmtop files.
>
> %FLAG LENNARD_JONES_ACOEF
> %FORMAT(5E16.8) (CN1(i), i=1,NTYPES*(NTYPES+1)/2)
> CN1 : Lennard Jones r**12 terms for all possible atom type interactions,
> indexed by ICO and IAC; for atom i and j where i < j, the index
> into
> this array is as follows (assuming the value of ICO(index) is
> positive):
> CN1(ICO(NTYPES*(IAC(i)-1)+IAC(j))).
>
> %FLAG LENNARD_JONES_BCOEF
> %FORMAT(5E16.8) (CN2(i), i=1,NTYPES*(NTYPES+1)/2)
> CN2 : Lennard Jones r**6 terms for all possible
> atom type interactions. Indexed like CN1 above.
>
>
> On Fri, Jan 6, 2017 at 4:09 PM, Jonathan Huihui <Jonathan.Huihui.du.edu>
> wrote:
>
> > So here's where I'm at so far:
> >
> >
> > I'm under the impression at this point that the L J A+B coefficients
> > aren't able to be modified for my purpose in the force-field itself,
> > however a post-processing of the .top file itself may yield something.
> >
> > My question is that after finding the section of the .top file where the
> > coefficients are listed, how are the A and B coefficients listed
> organized
> > in terms of atom type?
> >
> >
> > Thanks so much for any and all help so far!
> >
> >
> > Jonathan Huihui
> >
> > Graduate Student, University of Denver
> >
> > Department of Physics & Astronomy
> >
> > http://portfolio.du.edu/jhuihui2
> >
> > ________________________________
> > From: David A Case <david.case.rutgers.edu>
> > Sent: Thursday, December 22, 2016 6:18:25 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Force field modifications
> >
> > On Thu, Dec 22, 2016, Jonathan Huihui wrote:
> >
> > > http://ambermd.org/formats.html
> > >
> > > I have seen this page before and looked through it, however I've found
> > > it not very instructive in terms of syntax.
> >
> > We welcome specific suggestions for changes. Best thing to do is to go
> > through an existing parm.dat file while consulting the page above. That
> > should(?) make clear what information is stored, and what the details of
> > the
> > format are. Then you should be in a position to modify an existing
> > parm.dat
> > file, or to create one of your own.
> >
> > (If you don't understand Fortran format specifiers, just do a quick
> Google
> > search.)
> >
> > ....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Jan 06 2017 - 13:30:04 PST
