Dear Jagur,
I parameterized a CNT some years ago, but did it manually directly in
leap. Here the way I did it:
- divide the NT in repeating units (1 residue < 100 atoms), e.g. 1 ring
segment, and extra residue(s) for the ends. Take care that the atom
names in the pdb are the same for each repeated segment and unique (e.g.
C1-C99).
- load a pdb of 1 segment in (x)leap
- bondbydistance
- edit mol, manually changed atom type to CA, atom charge 0 if only C
atoms (neglecting polarizability), if you have an uncapped nanotube and
therefore need H-atoms (atom type: HA) in the ends you could either
guess the charges by comparing the parameters with the ones for known
hydrocarbons like e.g. Phe, or run a qm-calculation of the final
segment(s).
- saveoff
So maybe this could help. But I have to add that it took me some time to
deal with right atom names and other formal stuff, but in the end it worked.
Nadine
------------------------------------------------------------
Dr. Nadine Utz
Molecular Modelling& Bioinformatics Group, IRB Barcelona
On 08/19/2011 06:32 PM, Jagur Lambix wrote:
> Dear Amber users,
> I am trying to create the parameter of a Carbon Nano Tube (CNT) using the antechamber.
>
> I started with the making of the mol2 file for the CNT with the following command, however after more than 24 hours it hangs on like the following message.
> The CNT has 576 atoms in total.
>
>
>
> [user.compute-02]$ /usr/apps/amber11/AmberTools/bin/antechamber -i CNT.pdb -fi pdb -o CNT.mol2 -fo mol2 -c bcc -s 2
>
> The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
> Running: /usr/apps/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (17792) exceeds the defaut ring size (500), reallocate memory automatically
>
> Running: /usr/apps/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (17792) exceeds the defaut ring size (500), reallocate memory automatically
> Total number of electrons: 3456; net charge: 0
>
> Running: /usr/apps/amber11/bin/sqm -O -i sqm.in -o sqm.out
>
>
>
>
> Please let me know your inputs on this and how to solve the issue.
>
> Thanks
>
> Jagur
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Received on Fri Aug 19 2011 - 10:30:03 PDT
