Well, I'm no closer to solving my problem, but I have tweaked the PBD a
bit to make this file, which doesn't let he hydrogens come so close to one
another (I thought that may be part of the problem). Before, hydrogens
were coming within 1.75A of each other, now the closest two hydrogens not
within the same methyl group are coming is 2.34A.
ATOM 1 CD MPD X 1 -0.147 0.417 0.005
ATOM 2 CC MPD X 1 0.356 -1.005 0.005
ATOM 3 1HC MPD X 1 0.963 -1.177 -0.888
ATOM 4 2HC MPD X 1 0.963 -1.177 0.897
ATOM 5 CB MPD X 1 -0.817 -1.953 0.005
ATOM 6 OB MPD X 1 -1.605 -1.730 -1.153
ATOM 7 1HB MPD X 1 -1.064 -1.883 -1.947
ATOM 8 CF MPD X 1 -1.655 -1.716 1.236
ATOM 9 1HF MPD X 1 -2.662 -1.431 0.942
ATOM 10 2HF MPD X 1 -1.213 -0.919 1.829
ATOM 11 3HF MPD X 1 -1.696 -2.626 1.829
ATOM 12 CA MPD X 1 -0.314 -3.375 0.005
ATOM 13 1HA MPD X 1 0.293 -3.547 0.897
ATOM 14 2HA MPD X 1 0.293 -3.547 -0.888
ATOM 15 3HA MPD X 1 -1.164 -4.062 0.005
ATOM 16 CE MPD X 1 0.356 1.127 -1.227
ATOM 17 1HE MPD X 1 1.449 1.127 -1.227
ATOM 18 2HE MPD X 1 -0.008 0.612 -2.119
ATOM 19 3HE MPD X 1 -0.008 2.158 -1.227
ATOM 20 OD MPD X 1 0.326 1.085 1.162
ATOM 21 1HD MPD X 1 1.202 1.449 0.986
ATOM 22 HD MPD X 1 -1.565 0.417 0.005
END
But, alas, I still get complaints about the "bonds may not be correct."
% Warning: the assigned bond types may be wrong, please :
% (1) double check the structure (the connectivity) and/or
% (2) adjust atom valence penalty parameters in APS.DAT, and/or
% (3) increase MAXVASTATE in define.h and recompile bondtype.C
% (4) increase PSCUTOFF in define.h and recompile bondtype.C
% Be cautious, use a large value of PSCUTOFF (>10) will significantly
% increase the computer time
% Error: cannot run "/sb/apps/amber9/i686/exe/bondtype -i
% ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
% judgebondtype() of antechamber.c properly, exit
Thanks!
Dave
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Received on Sun Jan 27 2008 - 06:07:13 PST
