Dear jit mukherjee,
You have a CNT connecting a nucleobase trough a spacer based on
ethylene glycol.
I guess the spacer arm can be of different lengths...
How to handle large CNT?
How to treat chemical equivalencing in your molecule?
How to handle various analogs of your structure?
I would use R.E.D. and/or R.E.D. Server for that...
regards, Francois
> I am using the antechamber tool. But when typing the command
> $AMBERHOME/exe/antechamber -i filename.pdb -fi pdb -o prepin -fo prepi
> -c bcc -s 2, 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 (3880) 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
>
> and the program stops here. I am attaching my pdb file and the files
> generated.
> can you please tell me how to get rid of the problem?
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Received on Tue Jun 26 2012 - 01:30:03 PDT
