[gmx-users] Atom not found in residue while adding hydrogens

[Travis Craddock]

The pdb file is of tubulin (1JFF) and the added residue is a methionine
residue obtained from (1TUB).  The pdb2gmx command line was as follows:

pdb2gmx -ff G43a1 -f GDPTUB.pdb -o GDPTUB.gro -p GDPTUB.top

where is used the gromacs 96 forcefield.  I am currently using gromacs version
 3.3.2.  The output after the initial  header is as follows:

pening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Reading GDPTUB.pdb...
Read 2 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 2 chains and 0 blocks of water and 2 residues with 2 atoms

  chain  #res #atoms
  1 'A'     1      1  
  2 'B'     1      1  

All occupancies are one
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up GDPTUB.top to ./#GDPTUB.top.1#
Processing chain 1 'A' (1 atoms, 1 residues)
There are 1 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms....
Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat
6 out of 6 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CA not found in residue 1 while adding atom

-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.2
Source code file: genhydro.c, line: 304

Fatal error:
Atom CA not found in residue MET1 while adding hydrogens
-------------------------------------------------------

"Do You Have a Mind of Your Own ?" (Garbage)



> Travis Craddock wrote:
> > Hi All,
> > 
> > I modified an existing pdb file by adding a missing residue with coordinates
> > obtained from another pdb file of lower resolution.  I ran pdb2gmx and
> > received the following fatal error:
> > 
> > Atom CA not found in residue MET1 while adding hydrogens
> > 
> > Can someone please explain this error to me?
> 
> Maybe...If you provide your pdb2gmx command line, which force field you're 
> using, and which Gromacs version you're using.
> 
> -Justin
> 
> > 
> > Thanks,
> > Travis
> > 
> > 
> > Travis Craddock
> > Department of Physics         
> > University of Alberta
> > 
> > _______________________________________________
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> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> 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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Travis Craddock
Department of Physics         
University of Alberta