[AMBER] Segmentation fault

From: MASLYK, MACIEJ MARCIN <maciejmarcin.maslyk.ceu.es>
Date: Wed, 16 Mar 2011 16:50:36 +0100

Dear Amber users,

I'm trying to make tpp and xyz file of a crystal cell of phenylalanines. First, I generated mol2 file with antechamber and when trying to run parmchk I got message: "segmentation fault". When I tried to run directly tleap the same error appears after syntax "phe = loadmol2 file.mol2". Error message is as fallows:
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /usr/local/amber10/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> phe = loadmol2 Phe_nowat1.mol2
Loading Mol2 file: ./Phe_nowat1.mol2
Reading MOLECULE named P01
/usr/local/amber10/bin/tleap: line 8: 21638 Segmentation fault /usr/local/amber10/bin/teLeap -I/usr/local/amber10/dat/leap/prep -I/usr/local/amber10/dat/leap/lib -I/usr/local/amber10/dat/leap/parm -I/usr/local/amber10/dat/leap/cmd $*

I was running many times different jobs on my system and there was no problem. One difference is that now I have pdb and mol2 with 380 Phenylalanines not connected (from crystal structure) (previously I was always using one ligand and protein). I'm using Amber10 with Amber tools 1.3.

Take a look at my mol2 file if necessary (attached)
Please, help with this.

Thanks in advance.


Dr. Maciej Maslyk
Universidad San Pablo CEU
Urb. Montepríncipe, Ctra. Boadilla del Monte,
Km. 5.300, 28668 Madrid, España
Tel.- 91.372.64.31 - FAX.- 91.351.04.75

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Received on Thu Mar 17 2011 - 10:00:04 PDT
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