<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;color:#000000;"><div>Dear All,</div><div><br></div><div>I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT using Amber99, which has been used for such systems, and CNT atoms are modeled using sp2 carbon parameters.</div><div><br></div><div>But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, and Amber99 forcefield, I get this error:</div><div>Fatal Error: </div><div>Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while sorting atoms.</div><div><br></div><div>During the execution, it says "There are 1 chains and 0 blocks of water and 1 residues with 168 atoms" after analyzing pdb file.</div><div><br></div><div>So I suspect problem is that it reads carbon as a residue in my .pdb file. </div><div><br></div><div>If
this is the problem, then how do I make sure that it reads carbon as an atom and not a residue?</div><div><br></div><div>My .pdb file has entries of the form:</div><div>ATOM 1 C C A 1 4.039 ....</div><div>ATOM 2 C C A 1 3.97 ....</div><div><br></div><div>Thanks for your help,</div><div>Majid</div><div style="position:fixed"></div>
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