Dear Akshay,
How did you create the .prepi file? I did a test case where I used
antechamber to create the .prepi file. It didnt give any error message
when I loaded try2.pdb (Your try2.pdb file ends with a line like /M;
erase that line and check if that is responsible for the error message u
are getting).
Best,
PS: Use TER cards in your .pdb file to seperate your molecules; e.g. your
solute molecules and each water molecule.
On Fri, 6 Oct 2006, Akshay Patny wrote:
> 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.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.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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>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Oct 08 2006 - 06:07:34 PDT
