On Tue, May 20, 2014, Nelson Max wrote:
> I am hoping to modify Amber to add stronger hydrogen bond forces to
> constrain the preservation of the secondary structure I have already built
> before we start energy minimization, since there are collisions whose large
> forces can cause that secondary structure to be destroyed in the initial
> steps of the minimization. I looked at the constraints part of the
> AmberTools manual, and got the impression that those constraints were good
> for a separate kind of calculation, based on the NOE data from NMR, and
> that they could not be added to a force field minimization. If the can,
> please tell me how. If not, please help me with the problem below.
"NMR" constraints can include distances, and are often used to enforce
hydrogen bonding.
>
> [max.tree AmberTools]$ nab conjgrad.nab
> conjgrad.nab:21 Symbol HB_init not declared.
You have to "register" new functions in symbol.c and nabcode.h. The reason is
that nab accpets both "C-like" and "Fortran-like" calling sequences, and the
compiler has to know which is which in order to generate the proper code.
There's no real documentation, but just follow the example of other functions.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 22 2014 - 07:30:03 PDT
