[gmx-users] pdb does not work.
Joseph Johnson
helstreak at hotmail.com
Tue Jun 16 05:15:30 CEST 2009
Just as a test run I wanted to see if I could simulate 5 repeats of glycine. I give the command:
pdb2gmx -f PGly.pdb -p PGly.top -o PGly.gro
and I tell it to do:
0: GROMOS96 43a1 force field
The output I get is:
Program pdb2gmx, VERSION 3.3.1
Source code file: resall.c, line: 438
Fatal error:
Residue '1' not found in residue topology database
Why is it giving me this output? Here is my pdb file and thank you for your help :)
HETATM 1 C 1 -3.361 1.127 2.911 C
HETATM 2 H 1 0.919 3.113 3.939 H
HETATM 3 H 1 -0.857 0.007 3.031 H
HETATM 4 H 1 -3.184 0.097 4.698 H
HETATM 5 H 1 -5.242 0.080 2.911 H
HETATM 6 O 1 -4.328 0.360 0.373 O
HETATM 7 H 1 -5.934 2.635 1.818 H
HETATM 8 H 1 -6.637 2.054 -0.750 H
HETATM 9 H 1 -4.459 1.860 -2.600 H
HETATM 10 H 1 -5.242 -0.129 -4.291 H
HETATM 11 C 1 -5.524 2.053 -0.750 C
HETATM 12 H 1 -4.698 -2.790 -3.382 H
HETATM 13 H 1 -6.834 -4.217 -4.291 H
HETATM 14 H 1 -9.153 -2.809 -3.382 H
HETATM 15 H 1 -9.153 -4.576 -3.382 H
HETATM 16 H 1 -3.758 -0.655 -3.381 H
HETATM 17 O 1 -1.506 2.874 3.937 O
HETATM 18 O 1 0.594 2.197 3.939 O
HETATM 19 H 1 -0.858 0.009 4.849 H
HETATM 20 C 1 -0.722 1.955 3.939 C
HETATM 21 N 1 -5.355 -2.021 -3.382 N
HETATM 22 C 1 -1.227 0.533 3.939 C
HETATM 23 N 1 -2.677 0.534 3.939 N
HETATM 24 O 1 -2.756 1.649 2.005 O
HETATM 25 H 1 -5.240 1.655 3.818 H
HETATM 26 C 1 -4.870 1.129 2.910 C
HETATM 27 N 1 -5.352 1.811 1.725 N
HETATM 28 H 1 -5.152 3.102 -0.751 H
HETATM 29 C 1 -5.022 1.342 0.483 C
HETATM 30 N 1 -5.042 1.369 -1.934 N
HETATM 31 O 1 -6.068 -0.528 -1.354 O
HETATM 32 C 1 -5.373 0.058 -2.150 C
HETATM 33 C 1 -4.871 -0.654 -3.382 C
HETATM 34 O 1 -7.486 -1.352 -3.382 O
HETATM 35 H 1 -6.834 -4.217 -2.473 H
HETATM 36 C 1 -7.205 -3.693 -3.382 C
HETATM 37 N 1 -8.643 -3.693 -3.382 N
HETATM 38 C 1 -6.701 -2.270 -3.382 C
CONECT 1 24 23 26
CONECT 2 18
CONECT 3 22
CONECT 4 23
CONECT 5 26
CONECT 6 29
CONECT 7 27
CONECT 8 11
CONECT 9 30
CONECT 10 33
CONECT 11 8 28 29 30
CONECT 12 21
CONECT 13 36
CONECT 14 37
CONECT 15 37
CONECT 16 33
CONECT 17 20
CONECT 18 2 20
CONECT 19 22
CONECT 20 17 18 22
CONECT 21 12 33 38
CONECT 22 3 19 20 23
CONECT 23 4 22 1
CONECT 24 1
CONECT 25 26
CONECT 26 5 25 1 27
CONECT 27 7 26 29
CONECT 28 11
CONECT 29 6 27 11
CONECT 30 9 11 32
CONECT 31 32
CONECT 32 31 30 33
CONECT 33 10 16 32 21
CONECT 34 38
CONECT 35 36
CONECT 36 13 37 38 35
CONECT 37 14 15 36
CONECT 38 34 21 36
END
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