<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Csilla,<div><br></div><div>First of all let's say that there's no difference if you use cp2k standalone of you invoke it from another program.</div><div>Our convention is quite clear about it: a kind has a well defined charge. I.e. you can't provide an array of different charges</div><div>associated to the same kind.</div><div><br class="webkit-block-placeholder"></div><div>The problem is in the definition of your problem.</div><div><br class="webkit-block-placeholder"></div><div>So if you want some help, we need more details.</div><div>How did you generated the CHARMM parameter file? is it one of the standard publicly distributed?</div><div>or you generated it with external tools starting maybe from other brand topology files?</div><div>are you also providing a PSF or you rely on the internal topology builder?</div><div><br></div><div>I rarely used PSFGEN, so I cannot comment how helpful it would be in solving this problem.. But essentially,</div><div>with some lines of scripting, you can do the type conversion without getting mad (both for PDB, parameter file and so).</div><div><br class="webkit-block-placeholder"></div><div>let us know withe above informations if you need further help!</div><div><br></div><div>Thanks,</div><div>Teo</div><div><br class="webkit-block-placeholder"></div><div><div><div>On 12 May 2008, at 12:19, Csilla Varnai wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; ">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?</span></blockquote></div><br></div></body></html>