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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Received on Fri Jan 06 2017 - 13:30:04 PST
