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.
I started to modify example 19.3 of the AmberTools 13 manual to call a new
routine of my own, HB_init(FILE* fp), which should read in a list of
hydrogen bonds to be preserved, that is, pairs of hydrogen and oxygen atom
numbers from the .pdb file. I have attached the modified file conjgrad.nab,
as well as the modified files sff.c and sff.h that contain the new
HB_init() routine. I repeatedly did make in the ambeer12/AMberTools/src/sff
directory until things compiled correctly, and then did make in the amber12
directory. But then when I typed the command
nab conjgrad.nab
I got the error below.
[max.tree AmberTools]$ nab conjgrad.nab
conjgrad.nab:21 Symbol HB_init not declared.
nab2c failed!
Without the offending line
HB_init(fopen(argv[3], "r"));
in conjgrad.nab, the nab compilation went OK, and the optimization also ran
without errors. I have not used nab before, but I successfully modified the
old Amber force field this way about 6 to 10 years ago. Is there something
about function declarations or compilation of nab that I need to fix to add
new functions to it?
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- text/x-csrc attachment: sff.c
- text/x-chdr attachment: sff.h
Received on Tue May 20 2014 - 18:00:02 PDT
