[gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

[TJ Piggot]

Just a quick look at the ffG45a3.rtp shows that there is an entry for ADE, 
however the ADE entry is for Adenine.

For help with your problem check out:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

Tom

--On Friday, September 14, 2007 14:13:55 +0100 parichita parichita 
<parichitamajumdar at yahoo.co.in> wrote:

> Hi,
>
>      I have facing some problem when converting .pdb file to .gro and
> .top .
>  I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the
> pdb2gmx command and 45a3 forcefield .
>  Showing the fatal error:
>  Atom O in residue ADE 1 not found in rtp entry with 25 atoms
>               while sorting atoms
>  and
> Warning: 'ADMA' not found in residue topology database, trying to use
> 'ADE'
>  Warning: 'ADMA' not found in residue topology database, trying to use
> 'ADE
>
>
> but in  ffG45a3.rtp I could not found any ADE ...........
>  so I was confused ...
>  Please give me some suggession.
>  The format of my M6M.pdb is,
>
> ATOM      1  C5  ADMA    1       3.337   1.774  -8.944  1.00  0.00
> C
>  ATOM      2  O   ADMA    1       4.702   1.679  -8.463  1.00  0.00
> O
>  ATOM      3  C1  ADMA    1       5.227   0.338  -8.248  1.00  0.00
> C
>  ATOM      4  C2  ADMA    1       4.345  -0.412  -7.222  1.00  0.00
> C
>  ATOM      5  O2  ADMA    1       4.481   0.211  -5.965  1.00  0.00
> O
>  ATOM      6  C3  ADMA    1       2.854  -0.372  -7.633  1.00  0.00
> C
>  ATOM      7  O3  ADMA    1       2.063  -0.925  -6.611  1.00  0.00
> O
>  ATOM      8  C4  ADMA    1       2.367   1.065  -7.950  1.00  0.00
> C
>  ATOM      9  O4  ADMA    1       1.062   1.009  -8.476  1.00  0.00
> O
>  ATOM     10  C6  ADMA    1       3.018   3.281  -9.160  1.00  0.00
> C
>  ATOM     11  O6  ADMA    1       1.778   3.456  -9.811  1.00  0.00
> O
>  ATOM     12  H5  ADMA    1       3.271   1.274  -9.929  1.00  0.00
> H
>  ATOM     13  H1  ADMA    1       6.262   0.415  -7.876  1.00  0.00
> H
>  ATOM     14  H2  ADMA    1       4.685  -1.464  -7.133  1.00  0.00
> H
>  ATOM     15  HO2 ADMA    1       5.425   0.166  -5.725  1.00  0.00
> H
>  ATOM     16  H3  ADMA    1       2.727  -0.987  -8.546  1.00  0.00
> H
>  ATOM     17  HO3 ADMA    1       1.139  -0.907  -6.925  1.00  0.00
> H
>  ATOM     18  H4  ADMA    1       2.343   1.645  -7.006  1.00  0.00
> H
>  ATOM     19  HO4 ADMA    1       0.779   1.926  -8.640  1.00  0.00
> H
>  ATOM     20 1H6  ADMA    1       3.805   3.735  -9.772  1.00  0.00
> H
>  ATOM     21 2H6  ADMA    1       3.014   3.809  -8.202  1.00  0.00
> H
>  ATOM     22  H6  ADMA    1       1.654   4.401  -9.918  1.00  0.00
> H
>  ATOM     23  C5  ADMA    1B      5.806  -2.519 -10.516  1.00  0.00
> C
>  ATOM     24  O   ADMA    1B      6.529  -3.735 -10.196  1.00  0.00
> O
>  ATOM     25  C1  ADMA    1B      6.753  -4.668 -11.291  1.00  0.00
> C
>  ATOM     26  O1  ADMA    1B      7.522  -4.046 -12.268  1.00  0.00
> O
>  ATOM     27  C2  ADMA    1B      5.398  -5.107 -11.893  1.00  0.00
> C
>  ATOM     28  O2  ADMA    1B      4.700  -5.870 -10.935  1.00  0.00
> O
>  ATOM     29  C3  ADMA    1B      4.533  -3.881 -12.271  1.00  0.00
> C
>  ATOM     30  O3  ADMA    1B      3.254  -4.305 -12.671  1.00  0.00
> O
>  ATOM     31  C4  ADMA    1B      4.406  -2.866 -11.106  1.00  0.00
> C
>  ATOM     32  O4  ADMA    1B      3.754  -1.706 -11.569  1.00  0.00
> O
>  ATOM     33  C6  ADMA    1B      5.743  -1.655  -9.224  1.00  0.00
> C
>  ATOM     34  O6  ADMA    1B      5.227  -0.368  -9.490  1.00  0.00
> O
>  ATOM     35  H5  ADMA    1B      6.383  -1.951 -11.270  1.00  0.00
> H
>  ATOM     36  H1  ADMA    1B      7.300  -5.545 -10.905  1.00  0.00
> H
>  ATOM     37  HO1 ADMA    1B      7.013  -3.281 -12.602  1.00  0.00
> H
>  ATOM     38  H2  ADMA    1B      5.572  -5.738 -12.788  1.00  0.00
> H
>  ATOM     39  HO2 ADMA    1B      5.261  -6.638 -10.719  1.00  0.00
> H
>  ATOM     40  H3  ADMA    1B      5.014  -3.365 -13.126  1.00  0.00
> H
>  ATOM     41  HO3 ADMA    1B      2.756  -3.507 -12.928  1.00  0.00
> H
>  ATOM     42  H4  ADMA    1B      3.788  -3.323 -10.307  1.00  0.00
> H
>  ATOM     43  HO4 ADMA    1B      3.668  -1.103 -10.809  1.00  0.00
> H
>  ATOM     44 1H6  ADMA    1B      6.749  -1.553  -8.805  1.00  0.00
> H
>  ATOM     45 2H6  ADMA    1B      5.131  -2.153  -8.466  1.00  0.00
> H
>  TER
>
>
> thanks in advance ..............
>
> parichita...........
>
>
>
>
>
>
>
>
>
> Parichita Mazumder
> Junior Research Fellow
> C/O Dr. Chaitali Mukhopadhayay
> Department of Chemistry
> University of Calcutta
> 92,A P C Road
> Kolkata-700009
> India.
>
>
> __________________________________________________
> 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.