AMBER Archive (2008)

Subject: AMBER: initial command?

From: Anamika Awasthi (aawasthi28_at_gmail.com)
Date: Wed Feb 27 2008 - 06:01:51 CST

my first command is showing this -----> why?
tleap -s -f oxy.scr
-I: Adding /usr/local/Amber9/amber9//dat/leap/prep to search path.
-I: Adding /usr/local/Amber9/amber9//dat/leap/lib to search path.
-I: Adding /usr/local/Amber9/amber9//dat/leap/parm to search path.
-I: Adding /usr/local/Amber9/amber9//dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source oxy.scr.

Welcome to LEaP!
Sourcing: ./oxy.scr
----- Source: /usr/local/Amber9/amber9//dat/leap/cmd/leaprc.ff03
----- Source of /usr/local/Amber9/amber9//dat/leap/cmd/leaprc.ff03 done
Log file: ./leap.log
Loading parameters: /usr/local/Amber9/amber9//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/Amber9/amber9//dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
Loading library: /usr/local/Amber9/amber9//dat/leap/lib/ions94.lib
Loading library: /usr/local/Amber9/amber9//dat/leap/lib/solvents.lib
Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/Amber9/amber9//dat/leap/lib/all_amino03.lib
Loading parameters: /usr/local/Amber9/amber9//dat/leap/parm/frcmod.spce
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for SPC/E water
Loading PDB file: ./oxyt.pdb
  Added missing heavy atom: .R<CGLY 9>.A<OXT 8>
  total atoms in file: 68
  Leap added 68 missing atoms according to residue templates:
       1 Heavy
       67 H / lone pairs
Checking 'oxy'....
Warning: Close contact of 1.831870 angstroms between .R<ASN 5>.A<H 2> and
.R<CYS 6>.A<H 2>
Checking parameters for unit 'oxy'.
Checking for bond parameters.
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Checking for angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: CT - SH - SH
There are missing parameters.
check: Warnings: 1
Unit is OK.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Building angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: CT - SH - SH
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1769
!FATAL: Message: 1-4: cannot add bond 10 92
!
!ABORTING.

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