Hi there,<div><br></div><div>when using for example:</div><div><br></div><div>pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none</div><div><br></div><div>I got in the agQQQ.pdb, things like:</div><div>
<br></div><div><div>ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00 N</div><div>ATOM 16 1HE2 NGL 1 4.030 7.698 3.448 1.00 0.00 HE</div><div>ATOM 17 2HE2 NGL 1 5.066 7.449 2.048 1.00 0.00 HE</div>
<div>ATOM 18 C NGL 1 5.487 2.636 0.037 1.00 0.00 C</div></div><div><br></div><div>Notice the last column, in special the "HE". This is wrong!</div><div><br></div><div>For most programmes it's not a issue since they seem to ignore the last column but this column exist and has a propose.</div>
<div><br></div><div>And there programmes that observe this column, like openbabel. If converting this pdb to mol2 I got wrong structure since babel thinks I am dealing with Helium atoms.</div><div><br></div><div>In gmx 4.0.x the last column was never printed so never had this problem before.</div>
<div><br></div><div>Thanks,</div><div><br></div><div>Alan</div><div><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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