AMBER Archive (2009)

Subject: [AMBER] problem with parmchk

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Mon May 18 2009 - 08:59:51 CDT

Hello,
I am trying to do some antechamber calculations for a CNT system. I would
like to obtain the necessary files for using in xLeap (prep and frcmod).
What I did first was:

$AMBERHOME/exe/antechamber -i prueba_H.pdb -fi pdb -o cnt.mol2 -fo mol2 -c
bcc -s 2

In this calculation I obtained these warnings, but it gave me a correct
cnt.mol2 file:
-------------------------------------------------------------------
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /usr/opt/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 (8616) exceeds the defaut ring size (500),
reallocate memory automatically

Running: /usr/opt/amber9/exe/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 (8616) exceeds the defaut ring size (500),
reallocate memory automatically
Total number of electrons: 1752; net charge: 0

Running: $AMBERHOME/exe/divcon

Running: /usr/opt/amber9/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p /usr/opt/amber9/dat/antechamber/BCCPARM.DAT
-s 2 -j 1

Running: /usr/opt/amber9/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC
-i ANTECHAMBER_AM1BCC_PRE.AC

Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (8616) exceeds the defaut ring size (500),
reallocate memory automatically

Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (8616) exceeds the defaut ring size (500),
reallocate memory automatically
--------------------------------------------------------------------

The problem came when I did

$AMBERHOME/exe/parmchk -i cnt.mol2 -o cnt.frcmod -f mol2

no errors appeared, but the calculation finishes with "Segmentation fault".
The cnt.frcmod written is empty.

Please, does anybody has any idea of which could be the problem? Maybe the
system is too big...?

Thank you very much in advance, 

-- 
Rebeca García Fandiño
Molecular Modelling and Bioinformatics Group
Institut de Reçerca Biomèdica 
Parc Cientific de Barcelona
08028 Barcelona
rebeca_at_mmb.pcb.ub.es

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