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

[Justin A. Lemkul]

Travis Craddock wrote:
> 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

I think this line suggests the problem.  It appears that pdb2gmx is only finding 
2 atoms in your input .pdb file!  Check the formatting, naming, numbering, etc., 
but I suspect something has gone badly wrong in preparing your input.

-Justin

> 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
> 
> 

-- 
========================================

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

========================================