thankyou for ur reply.<br>exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is <br>Program pdb2gmx, VERSION 4.0<br>Source code file: pdb2gmx.c, line: 429<br><br>Fatal error:<br>
Atom C in residue NH2 6 not found in rtp entry with 3 atoms<br> while sorting atoms<br><br><br>this is my pdb in text editor<br>there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m getting the error mentioned above<br>
AUTHOR GENERATED BY OPEN BABEL 2.2.0
<br>ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00 0.00 C
<br>ATOM 2 C ACE 1 -2.354 -0.410 0.072 1.00 0.00 C
<br>ATOM 3 O ACE 1 -1.743 -1.403 -0.345 1.00 0.00 O
<br>ATOM 4 N ALA 2 -1.649 0.885 0.183 1.00 0.00 N
<br>ATOM 5 CA ALA 2 -0.244 1.035 -0.187 1.00 0.00 C
<br>ATOM 6 C ALA 2 0.221 2.456 0.023 1.00 0.00 C
<br>ATOM 7 O ALA 2 -0.530 3.334 0.466 1.00 0.00 O
<br>ATOM 8 CB ALA 2 -0.094 0.568 -1.645 1.00 0.00 C
<br>ATOM 9 N ALA 3 1.482 2.703 -0.281 1.00 0.00 N
<br>ATOM 10 CA ALA 3 2.069 4.031 -0.129 1.00 0.00 C
<br>ATOM 11 C ALA 3 3.519 4.033 -0.548 1.00 0.00 C
<br>ATOM 12 O ALA 3 4.081 3.015 -0.969 1.00 0.00 O
<br>ATOM 13 CB ALA 3 1.870 4.463 1.334 1.00 0.00 C
<br>ATOM 14 N ALA 4 4.149 5.189 -0.449 1.00 0.00 N
<br>ATOM 15 CA ALA 4 5.553 5.340 -0.819 1.00 0.00 C
<br>ATOM 16 C ALA 4 6.019 6.761 -0.609 1.00 0.00 C
<br>ATOM 17 O ALA 4 5.267 7.638 -0.166 1.00 0.00 O
<br>ATOM 18 CB ALA 4 5.704 4.872 -2.277 1.00 0.00 C
<br>ATOM 19 N ALA 5 7.279 7.008 -0.913 1.00 0.00 N
<br>ATOM 20 CA ALA 5 7.866 8.336 -0.760 1.00 0.00 C
<br>ATOM 21 C ALA 5 9.317 8.337 -1.179 1.00 0.00 C
<br>ATOM 22 O ALA 5 9.879 7.319 -1.601 1.00 0.00 O
<br>ATOM 23 CB ALA 5 7.668 8.768 0.703 1.00 0.00 C
<br>ATOM 24 N NHM 6 10.022 9.633 -1.069 1.00 0.00 N
<br>ATOM 25 C NHM 6 11.417 9.736 -1.462 1.00 0.00 C
<br>CONECT 1 2
<br>CONECT 2 3 4 1
<br>CONECT 3 2
<br>CONECT 4 5 2
<br>CONECT 5 8 6 4
<br>CONECT 6 9 5 7
<br>CONECT 7 6
<br>CONECT 8 5
<br>CONECT 9 10 6
<br>CONECT 10 11 9 13
<br>CONECT 11 12 14 10
<br>CONECT 12 11
<br>CONECT 13 10
<br>CONECT 14 15 11
<br>CONECT 15 18 16 14
<br>CONECT 16 19 15 17
<br>CONECT 17 16
<br>CONECT 18 15
<br>CONECT 19 20 16
<br>CONECT 20 21 19 23
<br>CONECT 21 22 24 20
<br>CONECT 22 21
<br>CONECT 23 20
<br>CONECT 24 25 21
<br>CONECT 25 24
<br>MASTER 0 0 0 0 0 0 0 0 25 0 25 0
<br>END
<br><br>Please help me out.<br><br>With regards <br>Bhawana<br>