<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Teo,<div><br></div><div>Thanks very much!</div><div>Best regards,</div><div><br></div><div>Csilla</div><div><br></div><div><br><div><div>On 7 May 2008, at 17:04, Teodoro Laino wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "> Dear Csilla,<div>you got exactly the point. </div><div>In CP2K we take the CHARMM convention where a type has associated a charge.</div><div>This is different from AMBER where the same type can have different charges.</div><div><br class="webkit-block-placeholder"></div><div>So the best thing to do is to redefine your types according the convention that a type</div><div>has a well defined charge (this most of the times is terribly easy.. just append a letter or a number to</div><div>the existing type).</div><div><br class="webkit-block-placeholder"></div><div>Cheers</div><div>Teo</div><div><br class="webkit-block-placeholder"></div><div>p.s.: even with PDB this won't necessarily work. I'm not TOTALLY sure but in case you define two different</div><div>charges for the same type, only the first one may be assigned to that type. The result is that the</div><div>charges of your system will be wrong. I will add a warning for handling this exception, though reading </div><div>the charges from the beta column of the PDB is not something really standard.</div><div><br><div><div>On 7 May 2008, at 17:55, Csilla Varnai wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">in case of peptides. Hence, I need to read in the charges. I have <span class="Apple-converted-space"> </span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">found only 1 way to do it so far, namely reading it from a PDB file. <span class="Apple-converted-space"> </span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">My problem is that in this case I loose the accuracy of the <span class="Apple-converted-space"> </span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">coordinates, since this format is fairly restricted and I cannot read <span class="Apple-converted-space"> </span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">the coordinates only at a +/-0.001 level.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Could anyone please help me, if there is a better way I've missed to <span class="Apple-converted-space"> </span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">get both the charges and the coordinates at a given accuracy?</font></div> </blockquote></div><br></div><br> <br> </div><br></blockquote></div><br></div></body></html>