Hi Justin, <div>the gromacs version is 4.0.4. </div><div>command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p 1B9Eostate.top -ff amber03</div><div>message: WARNING: atom H is missing in residue ILE 2 in the pdb file</div>
<div> You might need to add atom H to the hydrogen database of residue ILE</div><div> in the file ff???.hdb (see the manual)</div><div>beginning of pdb file:</div><div><div>ATOM 1 N NGLYA 1 -5.201 9.673 -2.852 1.00 21.99 N </div>
<div>ATOM 2 CA NGLYA 1 -3.724 9.368 -2.711 1.00 21.30 C </div><div>ATOM 3 C NGLYA 1 -3.320 8.030 -3.324 1.00 18.48 C </div><div>ATOM 4 O NGLYA 1 -4.164 7.323 -3.878 1.00 24.81 O </div>
<div>ATOM 5 N ILE A 2 -2.065 7.644 -3.159 1.00 13.65 N </div><div>ATOM 6 CA ILE A 2 -1.579 6.399 -3.716 1.00 12.18 C </div><div>ATOM 7 C ILE A 2 -2.254 5.174 -3.077 1.00 15.61 C </div>
<div>ATOM 8 O ILE A 2 -2.629 4.249 -3.786 1.00 13.09 O </div><div>ATOM 9 CB ILE A 2 -0.037 6.325 -3.601 1.00 12.48 C </div><div>ATOM 10 CG1 ILE A 2 0.494 5.122 -4.357 1.00 14.27 C </div>
<div>ATOM 11 CG2 ILE A 2 0.397 6.250 -2.171 1.00 7.71 C </div><div>ATOM 12 CD ILE A 2 1.946 5.193 -4.618 1.00 11.64 C </div><div>ATOM 13 N VAL A 3 -2.487 5.202 -1.759 1.00 19.67 N </div>
<div>ATOM 14 CA VAL A 3 -3.123 4.072 -1.065 1.00 21.16 C </div><div>ATOM 15 C VAL A 3 -4.531 3.814 -1.605 1.00 21.76 C </div><div>ATOM 16 O VAL A 3 -4.954 2.670 -1.806 1.00 20.69 O </div>
<div>ATOM 17 CB VAL A 3 -3.225 4.312 0.465 1.00 21.43 C </div><div>ATOM 18 CG1 VAL A 3 -3.687 3.033 1.165 1.00 21.34 C </div><div>ATOM 19 CG2 VAL A 3 -1.885 4.782 1.039 1.00 19.65 C </div>
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