[gmx-users] H211 in ffG53a5
Ken Rotondi
ksr at chemistry.umass.edu
Mon Apr 3 19:27:02 CEST 2006
Hello all,
I added the RNA hydrogens to my ffG53a5.hdb file, which eliminated the
H2*, etc. missing from .hdb file errors. However, when I run pdb2gmx on
a test .pdb file with one nucleotide in it returns a fatal error that:
"Atom H211 not found in rtp database in residue GUA, it looks a bit
like H21"
There is no H211 in either the .hdb or .pdb file.
Why is this error occurring?
How do I eliminate it?
Thanks,
Ken
Below are the lines I added to my ffG53a5.hdb file, the test.pdb file,
and the full pdb2gmx output.
_____________________
ADE 3
1 2 H2* O2* C2* C3*
2 3 H61 N6 C6 N1
2 3 H62 N6 C6 N1
GUA 4
1 2 H2* O2* C2* C3*
2 3 H21 N2 C2 N1
2 3 H22 N2 C2 N1
1 1 H1 N1 C6 C2
CYT 3
1 2 H2* O2* C2* C3*
2 3 H41 N4 C4 N3
2 3 H42 N4 C4 N3
URA 2
1 2 H2* O2* C2* C3*
1 1 H3 N3 C2 C4
_____________________
ATOM 1 P GUA A 1 4.006 48.703 126.810 1.00 58.91
ATOM 2 O2P GUA A 1 4.598 50.201 126.810 1.00 58.91
ATOM 3 O1P GUA A 1 3.130 48.474 125.479 1.00 58.91
ATOM 4 O5* GUA A 1 5.220 47.646 126.843 1.00 58.91
ATOM 5 C5* GUA A 1 6.464 48.349 126.894 1.00 58.91
ATOM 6 C4* GUA A 1 7.236 48.051 128.158 1.00 58.91
ATOM 7 O4* GUA A 1 7.567 46.637 128.194 1.00 58.91
ATOM 8 C1* GUA A 1 8.854 46.462 128.764 1.00 58.91
ATOM 9 N9 GUA A 1 9.716 45.855 127.755 1.00 58.91
ATOM 10 C4 GUA A 1 10.914 45.215 127.975 1.00 58.91
ATOM 11 N3 GUA A 1 11.509 45.032 129.173 1.00 58.91
ATOM 12 C2 GUA A 1 12.655 44.380 129.062 1.00 58.91
ATOM 13 N2 GUA A 1 13.383 44.113 130.156 1.00 58.91
ATOM 14 N1 GUA A 1 13.174 43.942 127.869 1.00 58.91
ATOM 15 C6 GUA A 1 12.580 44.119 126.624 1.00 58.91
ATOM 16 O6 GUA A 1 13.135 43.683 125.607 1.00 58.91
ATOM 17 C5 GUA A 1 11.350 44.818 126.728 1.00 58.91
ATOM 18 N7 GUA A 1 10.447 45.200 125.746 1.00 58.91
ATOM 19 C8 GUA A 1 9.496 45.810 126.400 1.00 58.91
ATOM 20 C2* GUA A 1 9.338 47.838 129.227 1.00 58.91
ATOM 21 O2* GUA A 1 8.990 48.036 130.582 1.00 58.91
ATOM 22 C3* GUA A 1 8.576 48.757 128.282 1.00 58.91
ATOM 23 O3* GUA A 1 8.414 50.063 128.828 1.00 58.91
______________________
analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 23 atoms
chain #res #atoms
1 'A' 1 23
All occupancies are one
Opening library file /usr/local/grothree/share/gromacs/top/ffG53a5.atp
Atomtype 57
Reading residue database... (ffG53a5)
Opening library file /usr/local/grothree/share/gromacs/top/ffG53a5.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
Residue 108
Sorting it all out...
Opening library file ffG53a5.hdb
Opening library file /usr/local/grothree/share/gromacs/top/ffG53a5-n.tdb
Opening library file /usr/local/grothree/share/gromacs/top/ffG53a5-c.tdb
Processing chain 1 'A' (23 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms....
Opening library file /usr/local/grothree/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
No N- or C-terminus found: this chain appears to contain no protein
Now there are 1 residues with 29 atoms
Making bonds...
Opening library file
/usr/local/grothree/share/gromacs/top/aminoacids.dat
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3
Source code file: add_par.c, line: 221
Fatal error:
Atom H211 not found in rtp database in residue GUA, it looks a bit like
H21
-------------------------------------------------------
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