I have tried the 6,6-armchair carbon nanotube with both ends
terminated with hydrogens, using the Antechamber tool in Amber and it
was successfully loaded. I have also simmulate it.
But,when I am using the carbon nanotube functionalised with 1 cooH
group at a surfave carbon of the nanotube, it is showing the message:
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (3840) exceeds the defaut ring size
(500), reallocate memory automatically
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 "/usr/local/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full"
in judgebondtype() of antechamber.c properly, exit
For the functionalisation, I have just changed the carbon atom
hybridisation(to which the COOH group is added) to SP3 from SP2 and
then added a COOH group to it.
Whats the problem here?
--
jit mukherjee
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Received on Fri May 25 2012 - 13:00:03 PDT
