Dear all,<br><br>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:<br><br>pdb2gmx -f test.pdb<br><br>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 <br>
<br>"Fatal error:<br>Residue '2' not found in residue topology database"<br><br>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.<br>
<br>HETATM 1 C 2 2 -4.438 3.334 2.988<br>HETATM 2 C 2 2 0.588 3.313 0.517<br>HETATM 3 C 2 2 5.476 3.310 -2.216<br>HETATM 4 H 2 2 -4.134 2.590 3.731<br>
HETATM 5 H 2 2 -5.525 3.438 3.047<br>HETATM 6 H 2 2 -3.996 4.291 3.276<br>HETATM 7 H 2 2 1.480 3.111 1.117<br>HETATM 8 H 2 2 -0.266 3.349 1.200<br>
HETATM 9 H 2 2 0.702 4.307 0.076<br>HETATM 10 H 2 2 6.375 3.525 -1.633<br>HETATM 11 H 2 2 4.648 3.862 -1.761<br>HETATM 12 H 2 2 5.628 3.709 -3.223<br>
HETATM 13 C 2 2 -3.996 2.922 1.581<br>HETATM 14 H 2 2 -2.902 2.862 1.545<br>HETATM 15 H 2 2 -4.281 3.703 0.865<br>HETATM 16 C 2 2 0.394 2.242 -0.557<br>
HETATM 17 H 2 2 -0.485 2.486 -1.167<br>.<br>.<br>.<br>.<br>.<br><br>Jacob Harvey<br clear="all"><br>-- <br>--<br>Jacob Harvey<br><br>Graduate Student<br><br>University of Massachusetts Amherst<br><br><a href="mailto:j.harv8@gmail.com">j.harv8@gmail.com</a><br>