[gmx-users] H211 in ffG53a5

Mon Apr 3 20:40:55 CEST 2006

David,

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.
> _____________________
> 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
> -------------------------------------------------------

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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 5149 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060403/a5c5a4b7/attachment.bin>