hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. * i m using forcefield ffgmx. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as: --------------------------------------------------------- Program pdb2gmx, VERSION 4.0 Source code file: pdb2top.c, line: 574
Fatal error: atom N not found in residue 1ACE while combining tdb and rtp ----------------------------------------------------- This is my pdb file in text editor AUTHOR GENERATED BY OPEN BABEL 2.2.0 ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00 0.00 C ATOM 2 C ACE 1 -2.354 -0.410 0.072 1.00 0.00 C ATOM 3 O ACE 1 -1.743 -1.403 -0.345 1.00 0.00 O ATOM 4 N ALA 2 -1.649 0.885 0.183 1.00 0.00 N ATOM 5 CA ALA 2 -0.244 1.035 -0.187 1.00 0.00 C ATOM 6 C ALA 2 0.221 2.456 0.023 1.00 0.00 C ATOM 7 O ALA 2 -0.530 3.334 0.466 1.00 0.00 O ATOM 8 CB ALA 2 -0.094 0.568 -1.645 1.00 0.00 C ATOM 9 N ALA 3 1.482 2.703 -0.281 1.00 0.00 N ATOM 10 CA ALA 3 2.069 4.031 -0.129 1.00 0.00 C ATOM 11 C ALA 3 3.519 4.033 -0.548 1.00 0.00 C ATOM 12 O ALA 3 4.081 3.015 -0.969 1.00 0.00 O ATOM 13 CB ALA 3 1.870 4.463 1.334 1.00 0.00 C ATOM 14 N ALA 4 4.149 5.189 -0.449 1.00 0.00 N ATOM 15 CA ALA 4 5.553 5.340 -0.819 1.00 0.00 C ATOM 16 C ALA 4 6.019 6.761 -0.609 1.00 0.00 C ATOM 17 O ALA 4 5.267 7.638 -0.166 1.00 0.00 O ATOM 18 CB ALA 4 5.704 4.872 -2.277 1.00 0.00 C ATOM 19 N ALA 5 7.279 7.008 -0.913 1.00 0.00 N ATOM 20 CA ALA 5 7.866 8.336 -0.760 1.00 0.00 C ATOM 21 C ALA 5 9.317 8.337 -1.179 1.00 0.00 C ATOM 22 O ALA 5 9.879 7.319 -1.601 1.00 0.00 O ATOM 23 CB ALA 5 7.668 8.768 0.703 1.00 0.00 C ATOM 24 N NAC 6 10.022 9.633 -1.069 1.00 0.00 N ATOM 25 CA NAC 6 11.417 9.736 -1.462 1.00 0.00 C CONECT 1 2 CONECT 2 3 4 1 CONECT 3 2 CONECT 4 5 2 CONECT 5 8 6 4 CONECT 6 9 5 7 CONECT 7 6 CONECT 8 5 CONECT 9 10 6 CONECT 10 11 9 13 CONECT 11 12 14 10 CONECT 12 11 CONECT 13 10 CONECT 14 15 11 CONECT 15 18 16 14 CONECT 16 19 15 17 CONECT 17 16 CONECT 18 15 CONECT 19 20 16 CONECT 20 21 19 23 CONECT 21 22 24 20 CONECT 22 21 CONECT 23 20 CONECT 24 25 21 CONECT 25 24 MASTER 0 0 0 0 0 0 0 0 25 0 25 0 END so pls help me out. i had taken my pdb file from INSIGHTII program. With Regards Bhawana
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