<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear all,</div><div><br></div><div>I have redefined the atomic types, and regenerated the CHARMM22 potential file according to the new atomic types, at first sight in a very simple-minded way, substituting all the possible new atomic types (say, CC1, CC2) into the old ones (CC). But in this case, due to the large potential file, running the program is hopeless.</div><div>I must confess I have not tried the VMD psfgen, since I would like to invoke CP2K from another program, and that is the reason why I would like to avoid the use of other programs like the VMD psfgen. If I used the cp2k f77_interface, would it make any difference concerning to this problem? Should I also have a potential file containing atomic types with unambiguously defined charges? If that is the case then I run into the same memory problem. Does the psfgen seem to be the only solution?</div><div>Best regards,</div><div><br></div><div>Csilla</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></body></html>