[gmx-users] Re: pdb2gmx fatal error - atom not found

[Justin A. Lemkul]

C Colenso wrote:
> Hi Justin,
> 
> I got your email from the Gromacs mailing list...I hope you don't mind.
> 
> I have a problem with pdb2gmx.
> 
> I have downloaded the 4.5.4 version of gromacs, no luck, I have consulted
> the mailing lists and bugzillas, and tried every suggestion but this is
> still not fixing my problem and I am getting rather frustrated now....
> 
> Please could you try and help....?
> 

I cannot serve as a private tutor; I reply to the list for the benefit of the 
community and to further discussion.  I receive far too many personal requests 
to keep up with them all.  I am CC'ing this message to the gmx-users list and 
would ask that you post anything further there.  That's why the mailing list exists.

> I am trying to output a .pdb from a .gro file using this command:
> 
> pdb2gmx -f herg_popc_L532P_md-2.gro -o herg_popc_L532P_md-2.pdb -chainsep
> id -ter
> 

This command will not work.  There are no chain identifiers in a .gro file, so 
this could be one source of breakdown.

> (I have tried using the -interactive and -ignh commands but this doesnt
> help either)
> 

Without seeing the remaining selections (force field, termini selection) I can't 
comment further about whether you're doing things right.

> The error message I get is:
> 
> Fatal error:
> Atom OXT in residue ALA 671 was not found in rtp entry ALA with 10 atoms
> while sorting atoms.
> 

This may be a consequence of the -chainsep option identifying something 
incorrectly.  Is there anything else in the input coordinate file after Ala671? 
  It appears from the coordinates below that it should indeed be a terminus, but 
there could be some confusion if there are other things in the .gro file.

> I have tried adding OXT to the .rtp...this didnt work
> 
> 

Nor should it.  Termini replacements are made by the .n.tdb and .c.tdb files; 
they handle renaming and atom addition/deletion.  You shouldn't need to change 
anything.

> This is a problem with the C-terminal ALA residue.....
> This is what it looks like in the .gro:
> 
>   671ALA      N 4423   9.361  10.928   5.227  0.1453 -0.0243 -0.1436
>   671ALA      H 4424   9.377  11.023   5.197  1.0816  0.3382  1.3859
>   671ALA     CA 4425   9.270  10.924   5.340  0.0567 -0.1974 -0.2220
>   671ALA     HA 4426   9.199  10.841   5.341 -2.2883  1.6603 -1.8477
>   671ALA     CB 4427   9.339  10.922   5.476  0.1011 -0.2943 -0.2457
>   671ALA    HB1 4428   9.267  10.946   5.555  1.2607  0.1822  0.7063
>   671ALA    HB2 4429   9.373  10.818   5.475  1.9064  0.2650 -1.6416
>   671ALA    HB3 4430   9.430  10.981   5.484 -0.8386  1.2073 -0.3433
>   671ALA      C 4431   9.178  11.045   5.338 -0.3791 -0.5290 -0.3389
>   671ALA     OT 4432   9.212  11.144   5.274 -0.3511 -0.0384  0.4190
>   671ALA      O 4433   9.074  11.040   5.426  0.0589 -0.2978  0.1970
>   671ALA     HO 4434   9.082  10.962   5.479 -1.1979  0.0008  0.8966
> 
> 
> I don't know what is going on with the C-term and why there are so many
> atoms.....OT,O and HO
> 

That's a normal (protonated) C-terminus.  OT is the carbonyl O, and O and H are 
the acidic portion of the -COOH terminus.

-Justin

> 
> If you could offer any suggestions I would be most grateful, I hope I have
> given you enough info...
> 
> Many thanks in advance
> 
> Charlie
> 
> 
> 
> 

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

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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