<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi,<br><br>I have just started to learn gromacs. I am facing a problem to make topology file of a myoglobin. I got the pdb file from the csc tutorial.<br><br>When i am running the pdb2gmx with<br><br>pdb2gmx -f conf.pdb -p topol.top<br><br>i get the message, HEME148 CAB1428 0.569<br> HEME148 CAC1437 0.562 0.820<br>N-terminus: NH3+<br>C-terminus: COO-<br>Now there are 148 residues with 1451 atoms<br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.1<br>Source code file: pdb2top.c, line: 570<br><br>Fatal error:<br>atom N not found in residue 1ACE while combining tdb and rtp<br>-------------------------------------------------------<br><br>I was using 43a1 force field (0), {but none of them works}.<br><br>i read
some previous post and got the idea that there should be a N atom with should be linked with ACE, but my conf.pdb files does not have any. I have topol.top file from the tutorial but didn't show how I can generate that.<br><br>I am a totally newbie, thus I am wondering what should I do. Which file I should correct to get rid of those? Do I need to know the bonding of every atom in the molecule for that?<br><br>Thanks in advance<br><br>Tawhid<br><br><br> <br></div></div></body></html>