Fwd: [gmx-users] Atom N21 not found

[Ken Rotondi]

Hi All,

More information. We ran pdb2gmx with the -debug flag. The outputs 
included the pdb2gmx.log file and a .pdb file. As can be seen below the 
error  occurs in the first nucleotide (GUA). Note in the output file, 
"chain_A.pdb", that atom 10 is correctly defined as  N2, while in the 
last line of the pdb2gmx.log file identifies atom 10 as N21. we believe 
the fatal error occurs In the routine "search_jtype", called from 
"name2type",  N2 was somehow defined as N21in the routine name2type, 
leading to the error.

(output .pdb file)
TITLE     GROtesk MACabre and Sinister
MODEL        1
ATOM      1  O5* GUA A   1       7.108 249.441 338.542  1.00  0.00
ATOM      2  C5* GUA A   1       7.168 248.860 339.827  1.00  0.00
ATOM      3  C4* GUA A   1       5.823 248.267 340.242  1.00  0.00
ATOM      4  O4* GUA A   1       4.843 249.287 340.342  1.00  0.00
ATOM      5  C1* GUA A   1       3.584 248.743 339.995  1.00  0.00
ATOM      6  N9  GUA A   1       3.046 249.392 338.786  1.00  0.00
ATOM      7  C4  GUA A   1       1.718 249.466 338.462  1.00  0.00
ATOM      8  N3  GUA A   1       0.676 248.933 339.163  1.00  0.00
ATOM      9  C2  GUA A   1      -0.519 249.193 338.608  1.00  0.00
ATOM     10  N2  GUA A   1      -1.634 248.724 339.181  1.00  0.00
ATOM     11  N1  GUA A   1      -0.668 249.935 337.446  1.00  0.00
ATOM     12  C6  GUA A   1       0.387 250.471 336.706  1.00  0.00
ATOM     13  O6  GUA A   1       0.167 251.093 335.672  1.00  0.00
ATOM     14  C5  GUA A   1       1.652 250.194 337.297  1.00  0.00
ATOM     15  N7  GUA A   1       2.922 250.551 336.868  1.00  0.00
ATOM     16  C8  GUA A   1       3.705 250.049 337.777  1.00  0.00
ATOM     17  C2* GUA A   1       3.796 247.263 339.750  1.00  0.00
ATOM     18  O2* GUA A   1       3.600 246.622 340.997  1.00  0.00
ATOM     19  C3* GUA A   1       5.253 247.186 339.318  1.00  0.00
ATOM     20  O3* GUA A   1       5.805 245.916 339.606  1.00  0.00

debug output last 10 lines (printed in name2type)

atom 1O5*: curcg=0, prevcg=-12345, cg=-12345
atom 2C5*: curcg=1, prevcg=-1, cg=0
atom 3C4*: curcg=2, prevcg=0, cg=1
atom 4O4*: curcg=3, prevcg=1, cg=2
atom 5C1*: curcg=3, prevcg=2, cg=2
atom 6N9: curcg=3, prevcg=2, cg=2
atom 7C4: curcg=4, prevcg=2, cg=3
atom 8N3: curcg=4, prevcg=3, cg=3
atom 9C2: curcg=5, prevcg=3, cg=4
atom 10N21: curcg=5, prevcg=4, cg=4

ERROR seen:

-----------------------------
Program pdb2gmx, VERSION 3.3_beta_20050202
Source code file: add_par.c, line: 221

Fatal error:
Atom N21 not found in rtp database in residue GUA, it looks a bit like 
N2
----------------------------


Begin forwarded message:
> Hello all,
>
> I'm trying to run pdb2gmx on a ribo-protein. I'm getting an extremely 
> strange error:
>
> The first nucleotide on the first chain is GUA and there is no N21 
> atom defined in it or anywhere else (we did a global search of the 
> file) in the .pdb file.
>
> What could be causing this error?
>
> Thanks as always,
>
> Ken
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
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