AMBER Archive (2008)

Subject: AMBER: silica slab

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Tue Feb 05 2008 - 11:28:55 CST

Hi,

I have problems preparing pure Si slab. I have constructed Si slab
(crystal), but when I run antechamber i get Error (liek below). how to
edit FF files to properly set Si slab for simulation ?

Arturas

>antechamber -i sislab.pdb -fi pdb -o sislab.mol2 -fo mol2 -s 2

The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /public/usr/lib/AMBER/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
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 "/public/usr/lib/AMBER/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit
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