[gmx-users] pdb does not work.
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Jun 16 05:48:03 CEST 2009
Joseph Johnson wrote:
> 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 :)
... because your PDB file does not name your residues. pdb2gmx isn't
magic - it depends on the residue name to recognize which entry in the
residue topology database (.rtp file) should be applied. So, read the
PDB format document to work out which columns should have "GLY", or use
a known-good PDB file to copy the right columns.
Mark
> 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
>
> ------------------------------------------------------------------------
> Lauren found her dream laptop. Find the PC that’s right for you.
> <http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users
mailing list