AMBER Archive (2006)

Subject: Re: AMBER: LEAP error

From: Scott Brozell (
Date: Fri Oct 06 2006 - 12:30:34 CDT


Gooooogggle-ing the error message would find amber8's bugfix 15.
The resulting LEaP will give more info in the error.
Follow the error message's advice and verify that the connection
atoms are correct.
Another possibility is that atoms got reordered somewhere in preparing
the inputs.


On Fri, 6 Oct 2006, Akshay Patny wrote:

> Dear Amber users
> I am trying to build a prmtop/inpcrd file which has a non-standard residue:
> 2 DMPC lipid molecules and few waters. So for DMPC molecule, I have carried
> out an antechamber calculation and got a parameter topology file (prepi).
> Now, when I load LEAP using ff03/gaff and prepi file for DMPC; and then try
> to load my compound pdb file, I get the following error listed at the end of
> output:
> PS: All of the atom names for my 2 DMPC molecules are unique. LEAP complains
> about C2M atom being not in the first list??? (see error below at the end)
> r0914_at_redwood:/ptmp/r0914/Angi_trial/amber/dmpc_amber_preparation> ls
> dmpc_288_mod.pdb DMPC_bcc.prep dmpc_water_try.pdb leap.log try1.inpcrd
> try1.pdb try1.prmtop try2.pdb
> r0914_at_redwood:/ptmp/r0914/Angi_trial/amber/dmpc_amber_preparation> tleap -s
> -f leaprc.ff03
> -I: Adding /usr/local/appl/Amber8/dat/leap/prep to search path.
> -I: Adding /usr/local/appl/Amber8/dat/leap/lib to search path.
> -I: Adding /usr/local/appl/Amber8/dat/leap/parm to search path.
> -I: Adding /usr/local/appl/Amber8/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source leaprc.ff03.
> Welcome to LEaP!
> Sourcing: /usr/local/appl/Amber8/dat/leap/cmd/leaprc.ff03
> Log file: ./leap.log
> Loading parameters: /usr/local/appl/Amber8/dat/leap/parm/parm99.dat
> Loading parameters: /usr/local/appl/Amber8/dat/leap/parm/frcmod.ff03
> Reading force field mod type file (frcmod)
> Loading library: /usr/local/appl/Amber8/dat/leap/lib/all_amino03.lib
> Loading library: /usr/local/appl/Amber8/dat/leap/lib/ions94.lib
> Loading library: /usr/local/appl/Amber8/dat/leap/lib/solvents.lib
> Loading library: /usr/local/appl/Amber8/dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/appl/Amber8/dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/appl/Amber8/dat/leap/lib/all_aminont94.lib
> > source leaprc.gaff
> ----- Source: /usr/local/appl/Amber8/dat/leap/cmd/leaprc.gaff
> ----- Source of /usr/local/appl/Amber8/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /usr/local/appl/Amber8/dat/leap/parm/gaff.dat
> > loadamberprep DMPC_bcc.prep
> Loading Prep file: ./DMPC_bcc.prep
> > check DMP
> Checking 'DMP'....
> Checking parameters for unit 'DMP'.
> Checking for bond parameters.
> Checking for angle parameters.
> Unit is OK.
> > try = loadpdb try2.pdb
> Loading PDB file: ./try2.pdb
> ERROR: Comparing atoms C1N, H41, H42, H43 to atoms C2M, C1N, H43, H41
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 120
> !FATAL: Message: Atom C2M is not in the first list
> !
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