AMBER Archive (2006)

Subject: AMBER: LEAP error

From: Akshay Patny (akshay17_at_olemiss.edu)
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
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)

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
!
!ABORTING.
____________________________________________________________________________
__________________________________________________________

Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: akshay17_at_olemiss.edu
Tel: 662-915-1286 (office); Web: www.olemiss.edu

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