Hi,<br> <br> I have facing some problem when converting .pdb file to .gro and .top .<br> I have a .pdb of alpha d-mannose (1-6) alpha d-mannose. I was using the pdb2gmx command and 45a3 forcefield .<br> Showing the fatal error:<br> <span style="color: rgb(127, 0, 63);">Atom O in residue ADE 1 not found in rtp entry with 25 atoms</span><br style="color: rgb(127, 0, 63);"> <span style="color: rgb(127, 0, 63);"> while sorting atoms<br> <span style="color: rgb(0, 0, 0);">and <br> <span style="color: rgb(127, 0, 63);">Warning: 'ADMA' not found in residue topology database, trying to use 'ADE'</span><br style="color: rgb(127, 0, 63);"> <span style="color: rgb(127, 0, 63);">Warning: 'ADMA' not found in residue topology database, trying to use 'ADE</span><br style="color: rgb(127, 0, 63);"> <span style="color: rgb(127, 0, 63);"> </span><br> <br> </span></span>but in
ffG45a3.rtp I could not found any ADE ...........<br> so I was confused ...<br> Please give me some suggession.<br> The format of my M6M.pdb is,<br> <br> ATOM 1 C5 ADMA 1 3.337 1.774 -8.944 1.00 0.00 C<br> ATOM 2 O ADMA 1 4.702 1.679 -8.463 1.00 0.00 O<br> ATOM 3 C1 ADMA 1 5.227 0.338 -8.248 1.00 0.00 C<br> ATOM 4 C2 ADMA 1
4.345 -0.412 -7.222 1.00 0.00 C<br> ATOM 5 O2 ADMA 1 4.481 0.211 -5.965 1.00 0.00 O<br> ATOM 6 C3 ADMA 1 2.854 -0.372 -7.633 1.00 0.00 C<br> ATOM 7 O3 ADMA 1 2.063 -0.925 -6.611 1.00 0.00 O<br> ATOM 8 C4 ADMA 1 2.367 1.065 -7.950
1.00 0.00 C<br> ATOM 9 O4 ADMA 1 1.062 1.009 -8.476 1.00 0.00 O<br> ATOM 10 C6 ADMA 1 3.018 3.281 -9.160 1.00 0.00 C<br> ATOM 11 O6 ADMA 1 1.778 3.456 -9.811 1.00 0.00 O<br> ATOM 12 H5 ADMA 1 3.271 1.274 -9.929 1.00
0.00 H<br> ATOM 13 H1 ADMA 1 6.262 0.415 -7.876 1.00 0.00 H<br> ATOM 14 H2 ADMA 1 4.685 -1.464 -7.133 1.00 0.00 H<br> ATOM 15 HO2 ADMA 1 5.425 0.166 -5.725 1.00 0.00 H<br> ATOM 16 H3 ADMA 1 2.727 -0.987 -8.546 1.00 0.00 H<br>
ATOM 17 HO3 ADMA 1 1.139 -0.907 -6.925 1.00 0.00 H<br> ATOM 18 H4 ADMA 1 2.343 1.645 -7.006 1.00 0.00 H<br> ATOM 19 HO4 ADMA 1 0.779 1.926 -8.640 1.00 0.00 H<br> ATOM 20 1H6 ADMA 1 3.805 3.735 -9.772 1.00 0.00 H<br> ATOM 21 2H6 ADMA
1 3.014 3.809 -8.202 1.00 0.00 H<br> ATOM 22 H6 ADMA 1 1.654 4.401 -9.918 1.00 0.00 H<br> ATOM 23 C5 ADMA 1B 5.806 -2.519 -10.516 1.00 0.00 C<br> ATOM 24 O ADMA 1B 6.529 -3.735 -10.196 1.00 0.00 O<br> ATOM 25 C1 ADMA 1B 6.753 -4.668 -11.291 1.00
0.00 C<br> ATOM 26 O1 ADMA 1B 7.522 -4.046 -12.268 1.00 0.00 O<br> ATOM 27 C2 ADMA 1B 5.398 -5.107 -11.893 1.00 0.00 C<br> ATOM 28 O2 ADMA 1B 4.700 -5.870 -10.935 1.00 0.00 O<br> ATOM 29 C3 ADMA 1B 4.533 -3.881 -12.271 1.00 0.00 C<br> ATOM 30
O3 ADMA 1B 3.254 -4.305 -12.671 1.00 0.00 O<br> ATOM 31 C4 ADMA 1B 4.406 -2.866 -11.106 1.00 0.00 C<br> ATOM 32 O4 ADMA 1B 3.754 -1.706 -11.569 1.00 0.00 O<br> ATOM 33 C6 ADMA 1B 5.743 -1.655 -9.224 1.00 0.00 C<br> ATOM 34 O6 ADMA 1B 5.227 -0.368 -9.490
1.00 0.00 O<br> ATOM 35 H5 ADMA 1B 6.383 -1.951 -11.270 1.00 0.00 H<br> ATOM 36 H1 ADMA 1B 7.300 -5.545 -10.905 1.00 0.00 H<br> ATOM 37 HO1 ADMA 1B 7.013 -3.281 -12.602 1.00 0.00 H<br> ATOM 38 H2 ADMA 1B 5.572 -5.738 -12.788 1.00 0.00 H<br> ATOM 39
HO2 ADMA 1B 5.261 -6.638 -10.719 1.00 0.00 H<br> ATOM 40 H3 ADMA 1B 5.014 -3.365 -13.126 1.00 0.00 H<br> ATOM 41 HO3 ADMA 1B 2.756 -3.507 -12.928 1.00 0.00 H<br> ATOM 42 H4 ADMA 1B 3.788 -3.323 -10.307 1.00 0.00 H<br> ATOM 43 HO4 ADMA 1B 3.668 -1.103 -10.809 1.00
0.00 H<br> ATOM 44 1H6 ADMA 1B 6.749 -1.553 -8.805 1.00 0.00 H<br> ATOM 45 2H6 ADMA 1B 5.131 -2.153 -8.466 1.00 0.00 H<br> TER<br> <br> <br> thanks in advance ..............<br> parichita...........<br> <br> <br> <div style="text-align:
right;"> <br> </div> <br><BR><BR><DIV>
<DIV><FONT face=arial color=#0000bf>Parichita Mazumder <BR>Junior Research Fellow <BR>C/O Dr. Chaitali Mukhopadhayay <BR>Department of Chemistry <BR>University of Calcutta <BR>92,A P C Road <BR>Kolkata-700009 <BR>India.</FONT></DIV></DIV><p> 
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