AMBER Archive (2006)

Subject: Re: AMBER: LEAP error

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Fri Oct 06 2006 - 18:17:05 CDT

Dear Scott

I have upgraded to Amber9 and I guess if the bug was related
to amber8, amber9 should perform better in terms of
reporting the error.

I got the following error this time.
__________________________________________________________
> try = loadpdb try2.pdb
Loading PDB file: ./try2.pdb
ERROR: Comparing atoms
        .R<DMP 1>.A<C1N 115>,
        .R<DMP 1>.A<H41 2>,
        .R<DMP 1>.A<H42 3>, and
        .R<DMP 1>.A<H43 4>
       to atoms
        .R<DMP 1>.A<C2M 5>,
        .R<DMP 1>.A<C1N 115>,
        .R<DMP 1>.A<H43 4>, and
        .R<DMP 1>.A<H41 2>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C2M from DMP did not match !
!
!ABORTING.
__________________________________________________________

PS: I have realized that this error comes if I am using more
than one monomer of DMPC molecule in the input pdb file e.g.
2 DMPC mols in try2.pdb

However, if I am using just one single monomer of DMPC e.g.
input_try1.pdb ... LEAP successfully generated pdb
(try1.pdb) and prmtop/inpcrd files (try1.prmtop and
try1.inpcrd).

Any suggestion why this should happen?

I look forward to hear from you.

Kind Regards
Akshay Patny (Olemiss)

> Hi,
>
> 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.
>
> Scott
>
> 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_prep
> > aration> 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_prep
> > aration> 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.
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