[gmx-users] Issues with my PDB file

[Justin A. Lemkul]

Jacob Harvey wrote:
> Dear all,
> 
> I appear to be having problems with my pdb file for gromacs. If someone 
> could help me out that would be awesome. I enter the following code to 
> run pdb2gmx:
> 
> pdb2gmx -f test.pdb
> 
> and then I select a force field. I have selected OPLS-AA/L all-atom 
> force field (2001 aminoacid dihedrals). Once I select the force field I 
> get the error
> 
> "Fatal error:
> Residue '2' not found in residue topology database"
> 

That one's pretty self-explanatory.  You can't expect pdb2gmx to be magic. 
Parameters have to exist in the force field .rtp file for each building block 
you want to use.  A residue named "2" is meaningless to pdb2gmx.

-Justin

> This is what my pdb file looks like (I've just posted the first 10-15 
> lines or so). Does anyone see where I am going wrong? Thank you very 
> much in advance.
> 
> HETATM    1  C     2     2      -4.438   3.334   2.988
> HETATM    2  C     2     2       0.588   3.313   0.517
> HETATM    3  C     2     2       5.476   3.310  -2.216
> HETATM    4  H     2     2      -4.134   2.590   3.731
> HETATM    5  H     2     2      -5.525   3.438   3.047
> HETATM    6  H     2     2      -3.996   4.291   3.276
> HETATM    7  H     2     2       1.480   3.111   1.117
> HETATM    8  H     2     2      -0.266   3.349   1.200
> HETATM    9  H     2     2       0.702   4.307   0.076
> HETATM   10  H     2     2       6.375   3.525  -1.633
> HETATM   11  H     2     2       4.648   3.862  -1.761
> HETATM   12  H     2     2       5.628   3.709  -3.223
> HETATM   13  C     2     2      -3.996   2.922   1.581
> HETATM   14  H     2     2      -2.902   2.862   1.545
> HETATM   15  H     2     2      -4.281   3.703   0.865
> HETATM   16  C     2     2       0.394   2.242  -0.557
> HETATM   17  H     2     2      -0.485   2.486  -1.167
> .
> .
> .
> .
> .
> 
> Jacob Harvey
> 
> -- 
> --
> Jacob Harvey
> 
> Graduate Student
> 
> University of Massachusetts Amherst
> 
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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

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