Dear Amber users,
I am trying to convert a CNT.pdb (has connection info) into prepin with
Antechamber (AmberTools 1.4), and then into prmtop.
The nanotube has 1200 atoms, with no charge, and is to be used in an
implicit solvent simulation. I need this LONG tube though I know it is a
large number.
I hope to avoid dividing the molecule into small segments ...
I think I need only to obtain the bond information and the carbon atom
property in the topology (I am not sure if 0 charge of carbon atom will
affect the implicit solvent simulation)
So, with antechamber:
*antechamber -i CNT.pdb -fi pdb -o CNT.prepin -fo prepi*
it said
Segmentation fault (core dumped)
I tried following steps:
1. remove the connection info, and leave only the coordinates
ATOM 1 C UNK 1 6.779 0.000 -7.369 1.00 0.00
ATOM 2 C UNK 1 6.631 1.410 -7.369 1.00 0.00
ATOM 3 C UNK 1 6.447 2.095 -6.141 1.00 0.00
2. change the pdb to mol2 with VEGA ZZ
1 C 6.7790 0.0000 -36.8450 C.1 1 UNK1
0.0000
2 C 6.6310 1.4100 -36.8450 C.1 1 UNK1
0.0000
3 C 6.4470 2.0950 -35.6170 C.ar 1 UNK1
0.0000
and then use mol2 parameters for antechamber
and I got similar error, especially that for mol2 mode, there is an
additional line:
"The atom number exceeds the MAXATOM, reallocate memory"
BTW: I have the topology information in Gromacs format, so is there any code
that can convert gromacs topo into amber topo?
Or, if there is any code that can produce amber topo for carbon nanotubes?
Any input is appreciated!
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 14 2010 - 11:30:03 PDT
