[gmx-users] Atom -C not found in residue MET1 while adding hydrogens

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hi ALL,
> 
> I have a protein pdb file generated using MODELLER. When I use the 
> pdb2gmx command on it, it throws the error:
> 

What is your pdb2gmx command line?  It looks like a -ter issue.

> Atom -C not found in residue MET1 while adding hydrogens
> and
> Atom OXT in residue LEU 404
> 

What is the error message related to Leu-404?

-Justin

> The initial and end of the pdb file is like this:
> ---------------------------------------------------------------------------------
> CRYST1  116.083  116.083  116.083  90.00  90.00  90.00 P 1           1
> ATOM      1  N   MET X   1      67.960  51.279  76.751  1.00  
> 0.00           
> ATOM      2  CA  MET X   1      67.510  49.899  76.451  1.00  
> 0.00           
> ATOM      3  CB  MET X   1      65.990  49.769  76.661  1.00  
> 0.00           
> ATOM      4  CG  MET X   1      65.570  49.959  78.111  1.00  
> 0.00           
> ATOM      5  SD  MET X   1      63.780  49.819  78.401  1.00  
> 0.00           
> ATOM      6  CE  MET X   1      63.370  51.379  77.561  1.00  
> 0.00           
> ATOM      7  C   MET X   1      67.840  49.539  75.041  1.00  
> 0.00           
> ATOM      8  O   MET X   1      68.870  49.949  74.511  1.00  
> 0.00           
> ATOM      9  N   ALA X   2      66.970  48.749  74.401  1.00  
> 0.00           
> ATOM     10  CA  ALA X   2      67.240  48.349  73.051  1.00  
> 0.00           
> ATOM     11  CB  ALA X   2      66.160  47.429  72.461  1.00  
> 0.00           
> ATOM     12  C   ALA X   2      67.290  49.579  72.221  1.00  0.00 
> .
> .
> .
> ATOM   3069  OD2 ASP X 403      43.890  88.349  36.411  1.00  
> 0.00           
> ATOM   3070  C   ASP X 403      42.590  84.299  34.251  1.00  
> 0.00           
> ATOM   3071  O   ASP X 403      41.820  84.059  33.321  1.00  
> 0.00           
> ATOM   3072  N   LEU X 404      42.790  83.449  35.281  1.00  
> 0.00           
> ATOM   3073  CA  LEU X 404      42.100  82.199  35.401  1.00  
> 0.00           
> ATOM   3074  CB  LEU X 404      42.250  81.559  36.791  1.00  
> 0.00           
> ATOM   3075  CG  LEU X 404      43.710  81.209  37.151  1.00  
> 0.00           
> ATOM   3076  CD1 LEU X 404      44.580  82.469  37.241  1.00  
> 0.00           
> ATOM   3077  CD2 LEU X 404      43.770  80.349  38.431  1.00  
> 0.00           
> ATOM   3078  C   LEU X 404      40.610  82.469  35.201  1.00  
> 0.00           
> ATOM   3079  O   LEU X 404      40.010  81.799  34.311  1.00  
> 0.00           
> ATOM   3080  OXT LEU X 404      40.050  83.329  35.931  1.00  0.00
> END
> --------------------------------------------------------------------------------------
> 
> How can I remove these errors? Do I need to modify the pdb file anyway?
> Any suggestion is welcome.
> 
> Regards,
> 
>  
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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