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 simmulated it.
But,when I am using the carbon nanotube functionalised with 1 cooH
group at a side wall 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. So, it was a doublet system.i.e., with
887 no. of electrons. In the case of non-functionalised 6,6-carbon
nanotube, no. of electrons were 888 and this was a singlet system and
loaded in antechamber successfully.
Whats the problem here with the carbon nanotube functionalised with
one COOH group? Is the problem arising from the spin
multiplicity,i.e., from the one unpaired electron? Please help me.
Thanks and regards in advance.
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Received on Mon May 28 2012 - 21:30:02 PDT
