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Just as a test run I wanted to see if I could simulate 5 repeats of glycine. I give the command:<br><br>pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro<br><br>and I tell it to do:<br><br>0: GROMOS96 43a1 force field<br><br>The output I get is:<br><br>Program pdb2gmx, VERSION 3.3.1<br>Source code file: resall.c, line: 438<br><br>Fatal error:<br>Residue '1' not found in residue topology database<br><br>Why is it giving me this output? Here is my pdb file and thank you for your help :)<br><br>HETATM 1 C 1 -3.361 1.127 2.911 C<br>HETATM 2 H 1 0.919 3.113 3.939 H<br>HETATM 3 H 1 -0.857 0.007 3.031 H<br>HETATM 4 H 1 -3.184 0.097 4.698 H<br>HETATM 5 H 1 -5.242 0.080 2.911 H<br>HETATM 6 O 1 -4.328 0.360 0.373 O<br>HETATM 7 H 1 -5.934 2.635 1.818 H<br>HETATM 8 H 1 -6.637 2.054 -0.750 H<br>HETATM 9 H 1 -4.459 1.860 -2.600 H<br>HETATM 10 H 1 -5.242 -0.129 -4.291 H<br>HETATM 11 C 1 -5.524 2.053 -0.750 C<br>HETATM 12 H 1 -4.698 -2.790 -3.382 H<br>HETATM 13 H 1 -6.834 -4.217 -4.291 H<br>HETATM 14 H 1 -9.153 -2.809 -3.382 H<br>HETATM 15 H 1 -9.153 -4.576 -3.382 H<br>HETATM 16 H 1 -3.758 -0.655 -3.381 H<br>HETATM 17 O 1 -1.506 2.874 3.937 O<br>HETATM 18 O 1 0.594 2.197 3.939 O<br>HETATM 19 H 1 -0.858 0.009 4.849 H<br>HETATM 20 C 1 -0.722 1.955 3.939 C<br>HETATM 21 N 1 -5.355 -2.021 -3.382 N<br>HETATM 22 C 1 -1.227 0.533 3.939 C<br>HETATM 23 N 1 -2.677 0.534 3.939 N<br>HETATM 24 O 1 -2.756 1.649 2.005 O<br>HETATM 25 H 1 -5.240 1.655 3.818 H<br>HETATM 26 C 1 -4.870 1.129 2.910 C<br>HETATM 27 N 1 -5.352 1.811 1.725 N<br>HETATM 28 H 1 -5.152 3.102 -0.751 H<br>HETATM 29 C 1 -5.022 1.342 0.483 C<br>HETATM 30 N 1 -5.042 1.369 -1.934 N<br>HETATM 31 O 1 -6.068 -0.528 -1.354 O<br>HETATM 32 C 1 -5.373 0.058 -2.150 C<br>HETATM 33 C 1 -4.871 -0.654 -3.382 C<br>HETATM 34 O 1 -7.486 -1.352 -3.382 O<br>HETATM 35 H 1 -6.834 -4.217 -2.473 H<br>HETATM 36 C 1 -7.205 -3.693 -3.382 C<br>HETATM 37 N 1 -8.643 -3.693 -3.382 N<br>HETATM 38 C 1 -6.701 -2.270 -3.382 C<br>CONECT 1 24 23 26<br>CONECT 2 18<br>CONECT 3 22<br>CONECT 4 23<br>CONECT 5 26<br>CONECT 6 29<br>CONECT 7 27<br>CONECT 8 11<br>CONECT 9 30<br>CONECT 10 33<br>CONECT 11 8 28 29 30<br>CONECT 12 21<br>CONECT 13 36<br>CONECT 14 37<br>CONECT 15 37<br>CONECT 16 33<br>CONECT 17 20<br>CONECT 18 2 20<br>CONECT 19 22<br>CONECT 20 17 18 22<br>CONECT 21 12 33 38<br>CONECT 22 3 19 20 23<br>CONECT 23 4 22 1<br>CONECT 24 1<br>CONECT 25 26<br>CONECT 26 5 25 1 27<br>CONECT 27 7 26 29<br>CONECT 28 11<br>CONECT 29 6 27 11<br>CONECT 30 9 11 32<br>CONECT 31 32<br>CONECT 32 31 30 33<br>CONECT 33 10 16 32 21<br>CONECT 34 38<br>CONECT 35 36<br>CONECT 36 13 37 38 35<br>CONECT 37 14 15 36<br>CONECT 38 34 21 36<br>END<br><br /><hr />Lauren found her dream laptop. <a href='http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290' target='_new'>Find the PC that’s right for you.</a></body>
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