Many thanks, but I've had this in AMBER for some time. I need to use a UAFF.
On Apr 3, 2006, at 1:27 PM, Ken Rotondi wrote:
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.
_____________________
<x-tad-smaller>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
-------------------------------------------------------
</x-tad-smaller>
On Apr 3, 2006, at 2:26 PM, David Mathog wrote:
I added the RNA hydrogens to my ffG53a5.hdb file, which eliminated the
H2*, etc. missing from .hdb file errors.
1. Use the Amber FF files instead. (Requires some hand editing
of the PDB file.)
2. Also build in my modifications to gromacs 3.3 from here
http://saf.bio.caltech.edu/pub/software/molbio/gromacs-cit-33.tar.gz
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