AMBER Archive (2006)

Subject: AMBER: LEAP error

From: Akshay Patny (
Date: Fri Oct 06 2006 - 11:49:42 CDT

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

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)

I look forward to hear from you.

Thanks and Regards
Akshay Patny (Olemiss)

r0914_at_redwood:/ptmp/r0914/Angi_trial/amber/dmpc_amber_preparation> clear
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

Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
Tel: 662-915-1286 (office); Web:

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