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
<[EMAIL PROTECTED]> 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.
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TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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