<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Be careful at the region where you are cutting the aminoacid. Cutting at the amide bond can be tricky because of the highly polarised bond.<div class="">Better to cut between CA and CB, i.e. cut a bond that is not highly polarised.</div><div class=""><br class=""></div><div class="">Regarding the charge, you’ll get an excess charge that correspond to the opposite of the sum of the classical charges of your QM atoms.</div><div class="">You can just modify your FF file to distribute the corresponding excess charge to the whole MM system.</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 01 Aug 2015, at 08:16, tarak karmakar <<a href="mailto:tarak...@gmail.com" class="">tarak...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">I think I have got the clue to the charge related issue. <br class=""></div>First thing I missed is one oxygen with a charge of -0.51. <br class=""></div><div class="">Now, the total charge in my classical system is +1.68.<br class=""></div>I checked in literature and found out that Gly, Ala, and Pro residues can not be cut up to CA, rather one should select the entire residue by using a backbone cut. In my system, there are two Gly residues that I selected up to the CA atom. If I add the N and HN of these residues the total classical charge is coming out to be +2.00. <br class=""></div><div class=""></div><div class=""><br class=""><br class=""></div><div class="">Regards,<br class=""></div><div class="">Tarak<br class=""></div><div class=""><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Jul 31, 2015 at 10:04 PM, tarak karmakar <span dir="ltr" class=""><<a href="mailto:tarak...@gmail.com" target="_blank" class="">tarak...@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class=""><div class="">Dear All,<br class=""></div>I am trying to study an enzymatic reaction of an enzyme using CP2K. While running the QM/MM simulation I notice the following,<br class=""><br class=""> CHARGE_INFO| Total Charge of the Classical System: 1.170000<br class=""> DFT| Charge -2<br class=""><br class=""></div>From an old post<br class=""><a href="https://groups.google.com/forum/#!searchin/cp2k/charge$20QM$2FMM/cp2k/1BGZ2N3fSKc/J9E5HjI1o4cJ" target="_blank" class="">https://groups.google.com/forum/#!searchin/cp2k/charge$20QM$2FMM/cp2k/1BGZ2N3fSKc/J9E5HjI1o4cJ</a><br class=""> I realize that the user should take care of the non-integer charge, if it is there. <br clear="all" class=""><div class=""><div class=""><div class=""><br class=""></div><div class="">In my system, the reaction substrates in the active site have a total -2 charge while the surrounding amino acids are all neutral. Thus in the DFT section I have mentioned the following,<br class="">&DFT<br class=""> CHARGE -2<br class=""> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS<br class=""> POTENTIAL_FILE_NAME ./GTH_POTENTIALS<br class=""><br class=""></div><div class="">I have checked my .psf file, and the sum of all the atomic charges of the system is zero.<br class=""></div><div class=""><br class=""></div><div class="">So, my query is whether the partial charge arises due to the inappropriate selection of amino acid fragments in the QM region? <br class=""></div><div class="">I would appreciate if someone could help me in this issue.<br class=""><br class=""></div><div class="">Thanks,<br class=""></div><div class="">Tarak<br class=""></div></div></div></div> </blockquote></div><br class=""></div></div><div class=""><br class="webkit-block-placeholder"></div> -- <br class=""> You received this message because you are subscribed to the Google Groups "cp2k" group.<br class=""> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" class="">cp2k+uns...@googlegroups.com</a>.<br class=""> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" class="">cp...@googlegroups.com</a>.<br class=""> Visit this group at <a href="http://groups.google.com/group/cp2k" class="">http://groups.google.com/group/cp2k</a>.<br class=""> For more options, visit <a href="https://groups.google.com/d/optout" class="">https://groups.google.com/d/optout</a>.<br class=""> </div></blockquote></div><br class=""></div></body></html>