[gmx-users] Issues with my PDB file

[Jacob Harvey]

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"

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
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