AMBER Archive (2003)

Subject: Tleap

From: chandran karunakaran (ckaru2000_at_yahoo.com)
Date: Tue Apr 08 2003 - 18:01:21 CDT


Dear AMBER users,

  I attempted to run tleap for plastocyanin.
I hereby attach the command I gave and the
output given by the program. Would you
kinldy inform what should I do to overcome
this? With thanks

Sincerely Dr. C.Karunakaran

[amkumar_at_mcwsimsofa ~/karan]$ tleap -f leapp.in
-I: Adding /home/amkumar/soft/amber6/dat to search
path.
-I: Adding /home/amkumar/soft/amber6/dat/leap/lib to
search path.
-I: Adding /home/amkumar/soft/amber6/dat/leap/cmd to
search path.
-f: Source leapp.in.

Welcome to LEaP!
Sourcing leaprc:
/home/amkumar/soft/amber6/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters:
/home/amkumar/soft/amber6/dat/parm94.dat
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_nucleic94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_amino94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_aminoct94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_aminont94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/ions94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/water.lib
Sourcing: ./leapp.in
Loading parameters: ./frcmodp.pcy
Reading force field mod type file (frcmod)
Loading Prep file: ./mem.in
** 0.00000
                    : 'IMPROPER' atom N not found
82 pairs of atoms within potential bonding distance
54 are not H-H pairs
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<C 15> has maximum number of bonds.
Atom .R<2 1>.A<CB 4> has maximum number of bonds.
Atom .R<2 1>.A<CG 7> has maximum number of bonds.
Atom .R<2 1>.A<CG 7> has maximum number of bonds.
Atom .R<2 1>.A<C 15> has maximum number of bonds.
Atom .R<2 1>.A<C 15> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<C 15> has maximum number of bonds.
Atom .R<2 1>.A<CB 4> has maximum number of bonds.
Atom .R<2 1>.A<CG 7> has maximum number of bonds.
Atom .R<2 1>.A<SD 10> has maximum number of bonds.
Atom .R<2 1>.A<SD 10> has maximum number of bonds.
Atom .R<2 1>.A<HB2 5> has maximum number of bonds.
Atom .R<2 1>.A<HB3 6> has maximum number of bonds.
Atom .R<2 1>.A<HG2 8> has maximum number of bonds.
Atom .R<2 1>.A<HG3 9> has maximum number of bonds.
Atom .R<2 1>.A<C 15> has maximum number of bonds.
Atom .R<2 1>.A<C 15> has maximum number of bonds.
Atom .R<2 1>.A<HE1 12> has maximum number of bonds.
Atom .R<2 1>.A<HE2 13> has maximum number of bonds.
Atom .R<2 1>.A<HE3 14> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<SD 10> has maximum number of bonds.
Atom .R<2 1>.A<SD 10> has maximum number of bonds.
Atom .R<2 1>.A<CG 7> has maximum number of bonds.
Atom .R<2 1>.A<CG 7> has maximum number of bonds.
Atom .R<2 1>.A<HG2 8> has maximum number of bonds.
Atom .R<2 1>.A<HG3 9> has maximum number of bonds.
Atom .R<2 1>.A<SD 10> has maximum number of bonds.
Atom .R<2 1>.A<CE 11> has maximum number of bonds.
Atom .R<2 1>.A<HE3 14> has maximum number of bonds.
Atom .R<2 1>.A<HE1 12> has maximum number of bonds.
Atom .R<2 1>.A<CE 11> has maximum number of bonds.
Atom .R<2 1>.A<CE 11> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<SD 10> has maximum number of bonds.
Atom .R<2 1>.A<CE 11> has maximum number of bonds.
Atom .R<2 1>.A<CE 11> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Atom .R<2 1>.A<HE2 13> has maximum number of bonds.
Atom .R<2 1>.A<O 16> has maximum number of bonds.
Unexpected EOF: discarding residue ()
!FATAL ERROR----------------------------------------
!FATAL: In file [varArray.c], line 156
!FATAL: Message: VarArrayDestroy: VARARRAY is
NULL!
!ABORTING.
Abort (core dumped)

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