Hello dac,
Thanks for your kind reply but perhaps I did not ask right question.
Actually I want radii information file in Amber library for PB calculation.
Thanks.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
On Sat, Apr 7, 2018 at 8:39 PM, David A Case <david.case.rutgers.edu> wrote:
> On Sat, Apr 07, 2018, Rakesh Srivastava wrote:
> >
> > It will be very helpful if someone could tell where in the Amber library
> I
> > can get the atomic radii data for all atoms of amino acids.
>
> I think you should be careful here: the concept of "atomic radius" only
> transfers somewhat to force fields. If you want to compute the minimum
> energy distance between two atom types, you can add their Lennard-Jones
> radii, which are mostly found in $AMBERHOME/dat/leap/parm/parm10.dat
> (for ff14SB; look in leaprc.protein.xxxx for other protein force
> fields). You will have to manually connect atoms types to actual atom
> names by looking at the .lib files in $AMBERHOME/dat/leap/lib.
>
> But this is only one, special, definiation of "atomic radius". Be sure
> it is the one you want.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 07 2018 - 22:00:02 PDT
