Ah, sorry for the hasty reply, I should have looked more carefully. It
appears as though you're using AmberTools 1.2. Please go to
http://ambermd.org and download/install AmberTools 1.4 (free), as it is more
updated and has numerous bug fixes (such as eliminating segfaults with
tleap).
Hope this helps,
Jason
On Wed, Mar 16, 2011 at 8:50 AM, MASLYK, MACIEJ MARCIN <
maciejmarcin.maslyk.ceu.es> wrote:
> 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.
>
> Maciek
>
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 17 2011 - 10:00:08 PDT
