[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms

[Mark Abraham]

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Wednesday, June 2, 2010 6:18
Subject: Re: [gmx-users] Fatal error: Atom O in residue CO 1 not found in	rtp entry with 3 atoms  while sorting atoms
To: Gromacs Users' List <gmx-users at gromacs.org>

> 
> Nilesh Dhumal wrote:
> >I have addes the "CO" residue.
> >Coordinate file
> >
> >REMARK   Accelrys Discovery Studio PDB file
> >REMARK   Created:  Fri May 28 17:26:23 Eastern 
> Daylight Time 2010
> >HETATM    1  C1  
> CO     0      -
> 1.044  -0.027   0.066  0.00  
> 0.00           C
> >HETATM    2  O2  
> CO     0      -
> 0.009   0.642  -0.037  0.00  
> 0.00           O
> >HETATM    3  O3  
> CO     0      -
> 2.286   0.595  -0.030  0.00  
> 0.00           O
> >END
> >
> >in ffopla.rtp file.
> >
> >[ CO ] ; mandatory
> >[ ATOMS ] ; mandatory
> > C1   opls_974    1.00   1
> > O2   opls_975   -0.50   2
> > O3   opls_976   -0.50   2
> >
> >[ bonds ]
> > C1 O2
> > C1 O3
> >
> >I have also addes new atoms typs in ffopls.atp file.
> >
> 
> These input files work fine for me.  The error message 
> complained about an atom
> named "O" so be sure you're using the input you think you 
> are.  Something has
> gotten confused somewhere.

Perhaps the .pdb has column-formatting problems. Also, naming carbon dioxide "CO" and having two distinct atom types for its oxygen atoms, with non-neutral charge groups seems like asking for trouble...

Mark

> 
> -Justin
> 
> >NIlesh
> >
> >On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
> >
> >>Nilesh Dhumal wrote:
> >>
> >>>Hello,
> >>>
> >>>
> >>>I am getting the following error during pdb2gmx.
> >>>
> >>>
> >>>Fatal error: Atom O in residue CO 1 not found in rtp entry 
> with 3 atoms
> >>> while sorting atoms
> >>>
> >>>I checked the pdb file and ffopls.rtp file also.
> >>>
> >>>
> >>And what did you find?  To my knowledge there is no such 
> residue "CO" in
> >>the ffoplsaa.rtp file.  Is this something you've 
> added?  Regardless,
> >>there's a mismatch somewhere, so if you can't identify it, 
> post the text
> >>of your coordinate file and the relevant .rtp entry to see if 
> someone else
> >>can spot it.
> >>
> >>-Justin
> >>
> >>
> >>>Nilesh
> >>>
> >>>
> >>>
> >>>
> >>>
> >>--
> >>========================================
> >>
> >>
> >>Justin A. Lemkul
> >>Ph.D. Candidate
> >>ICTAS Doctoral Scholar
> >>MILES-IGERT Trainee
> >>Department of Biochemistry
> >>Virginia Tech
> >>Blacksburg, VA
> >>jalemkul[at]vt.edu | (540) 231-9080
> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >>
> >>========================================
> >>--
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> >>
> >
> >
> >
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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