AMBER Archive (2005)

Subject: Re: AMBER: xleap with modified residue

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Thu Oct 20 2005 - 13:25:41 CDT

I asked a similar question earlier this year. I don't recall exactly how I
fixed the problem, but here is the reply from the AMBER listserv that I used
to get started (see question and answer pasted below):

On Wed, May 25, 2005, Kenley Barrett wrote:
>
> I have what is probably a stupid question. I am receiving the
> following error upon trying to read a pdb file into XLeap:
>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 121
> !FATAL: Message: Atom N12 is not in the first list
> !
>
> What is the chirality.c file? I have been looking around in the
> various Amber directories and couldn't find it. Also, if anyone has
> experience dealing with this particular error, advice would be
> welcome.

Have you applied bugfix.15? That improves the error message, and often helps
identify the problem. If that doesn't help, you will probably have to post
your pdb file. But you could certainly look for an atom named "N12" and see
if there is anything odd about it or its environment.

The chirality.c file is in $AMBERHOME/src/leap/src/leap.

On 10/20/05, Whitney Allen <whitneygallen_at_yahoo.com> wrote:
>
> Hi Amber users
>
> I am trying to run MD on a TRNA structure (6tna.pdb). This molecule has
> several modified bases and so I have used Antechamber to compute a molecule
> library for each modified base. However, after loading the library file
> into xleap (which is successful) I try and load the TRNA structure and xleap
> completely shuts down.
>
> Below is the procedure that I follow. Note that I have tried to follow
> tutorials 4 & 5 as applicable. Here, for simplicity, I have cut the TRNA
> PDB file so that it contains only one modified residue (2MG or residue 10 in
> the 6tna.pdb file) and 15 total residues (residues 1-15 in the 6tna.pdbfile) and have called it
> test.pdb. If anyone can help please reply and I can send you the 2MG.pdb,
> 2MG.mol2, 2mg.lib, and test.pdb files.
>
> (*Antechamber- note that I change the residue to a molecule*)
>
> % $AMBERHOME/exe/antechamber -i 2MG.pdb -fi pdb -o 2MG.mol2 -fo mol2 -c
> bcc -s 2 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=LBFGS XTEST=0.0001"
>
> % $AMBERHOME/exe/parmchk –i 2MG.mol2 –f mol2 –o 2MG.frcmod
>
> % xleap –f leaprc.rna.ff99
>
> source leaprc.gaff
>
> loadmol2 2MG.mol2
>
> check 2MG
>
> edit 2MG
>
> loadamberparms 2MG.frcmod
>
> check 2MG
>
> saveoff 2MG.lib
>
> desc 2MG
>
> % xleap –f leaprc.rna.ff99
>
> source leaprc.gaff
>
> loadoff 2mg.lib
>
> check 2MG
>
> mol=loadpdb test.pdb
>
> (*At* *this point xleap closes and I get the following error*)
>
> !FATAL ERROR----------------------------------------
>
> !FATAL: In file [chirality.c], line 120
>
> !FATAL: Message: Atom P is not in the first list
>
> !
>
> !ABORTING.
>
> Please help me understand what is going on here and let me know how I can
> get this to work. It looks like all of the files are of normal format so I
> am a bit confused.
>
> Thanks in advance
>
> Whitney Hastings
>
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