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 [email protected]
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