<div dir="ltr"><div>From a QM/MM tutorial in amber,<br> <a href="http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-qm-mm/qm-min.out">http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-qm-mm/qm-min.out</a><br></div>I have got the following,<br><div><div><br> Sum of charges from parm topology file = -1.00010025<br>QMMM: ADJUSTING CHARGES<br>QMMM: ----------------------------------------------------------------------<br>QMMM: adjust_q = 2<br>QMMM: Uniformally adjusting the charge of MM atoms to conserve total charge.<br>QMMM: qm_charge = -1<br>QMMM: QM atom RESP charge sum (inc MM link) = -0.590<br>QMMM: Adjusting each MM atom resp charge by = 0.000<br>QMMM: Sum of MM + QM region is now = 0.000<br>QMMM: ----------------------------------------------------------------------<br><br></div><div>The charge has been adjusted automatically in the MM atoms. <br><br></div><div>Does CP2K has this kind of procedure?<br><br><br></div><div>Thanks,<br></div><div>Tarak<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Aug 1, 2015 at 1:19 PM, tarak karmakar <span dir="ltr"><<a href="mailto:tarak...@gmail.com" target="_blank">tarak...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Thanks Teo for the quick reply and suggestion.<br></div><div>What would you recommend for the GLY residue?<br></div><div>Is a cut in the CA-C bond a good choice for GLY?<br></div><div><br></div>In my system, I have two consecutive residues CYS 99 and GLY 100 in the active site which I need to include in the QM part. <br>Now, what I did as of now is, I cut a bond <br>i) between N of Ser 98 (previous residue) and CA of CYS 99.<br></div></div>ii) between CA of GLY 100 and C of GLY 100<br><div><div><br>While I do the above, I have got a non-integer charge of +1.68 for the classical part. <br></div><div>I calculated the sum of the atomic charges (atoms I selected for the QM part) and got +0.32.<br><br>-----------------------------------------------------------------------------------<br> 2707 99 CYS CA CT1 0.070000 12.0110 0<br> 2708 99 CYS HA HB1 0.090000 1.0080 0<br> 2709 99 CYS CB CT2 -0.110000 12.0110 0<br> 2710 99 CYS HB1 HA2 0.090000 1.0080 0<br> 2711 99 CYS HB2 HA2 0.090000 1.0080 0<br> 2712 99 CYS SG S -0.230000 32.0600 0<br> 2713 99 CYS HG1 HS 0.160000 1.0080 0<br> 2714 99 CYS C C 0.510000 12.0110 0<br> 2715 99 CYS O O -0.510000 15.9990 0<br></div><div>------------------------------------------------------------------------------------------Total= 0.16<br></div><div> 1043 100 GLY CA CT2 -0.020000 12.0110 0<br> 1044 100 GLY HA1 HB2 0.090000 1.0080 0<br> 1045 100 GLY HA2 HB2 0.090000 1.0080 0<br> 1046 100 GLY C C 0.510000 12.0110 0<br> 1047 100 GLY O O -0.510000 15.9990 0<br></div><div>----------------------------------------------------------------------------------- Total = 0.16<br></div><div><br></div><div>The total charge in the QM part is -2.<br><br></div><div>So, I will get an excess charge of +0.32 (or opposite, -0.32) from the atoms described in the QM part, right?<br></div><div>Distribute this excess charge in the MM part, does that mean I need to adjust the charges of the MM atoms in the .psf file to make my system neutral?<br></div><div><br><br></div><div>Thanks,<br></div><div>Tarak<br></div><div><br></div></div><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Aug 1, 2015 at 12:35 PM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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>Better to cut between CA and CB, i.e. cut a bond that is not highly polarised.</div><div><br></div><div>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>You can just modify your FF file to distribute the corresponding excess charge to the whole MM system.</div><div><br></div><div><br><div><blockquote type="cite"><div><div><div>On 01 Aug 2015, at 08:16, tarak karmakar <<a href="mailto:tarak...@gmail.com" target="_blank">tarak...@gmail.com</a>> wrote:</div><br></div></div><div><div><div><div dir="ltr"><div><div><div>I think I have got the clue to the charge related issue. <br></div>First thing I missed is one oxygen with a charge of -0.51. <br></div><div>Now, the total charge in my classical system is +1.68.<br></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></div><div></div><div><br><br></div><div>Regards,<br></div><div>Tarak<br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 31, 2015 at 10:04 PM, tarak karmakar <span dir="ltr"><<a href="mailto:tarak...@gmail.com" target="_blank">tarak...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Dear All,<br></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><br> CHARGE_INFO| Total Charge of the Classical System: 1.170000<br> DFT| Charge -2<br><br></div>From an old post<br><a href="https://groups.google.com/forum/#!searchin/cp2k/charge$20QM$2FMM/cp2k/1BGZ2N3fSKc/J9E5HjI1o4cJ" target="_blank">https://groups.google.com/forum/#!searchin/cp2k/charge$20QM$2FMM/cp2k/1BGZ2N3fSKc/J9E5HjI1o4cJ</a><br> I realize that the user should take care of the non-integer charge, if it is there. <br clear="all"><div><div><div><br></div><div>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>&DFT<br> CHARGE -2<br> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS<br> POTENTIAL_FILE_NAME ./GTH_POTENTIALS<br><br></div><div>I have checked my .psf file, and the sum of all the atomic charges of the system is zero.<br></div><div><br></div><div>So, my query is whether the partial charge arises due to the inappropriate selection of amino acid fragments in the QM region? <br></div><div>I would appreciate if someone could help me in this issue.<br><br></div><div>Thanks,<br></div><div>Tarak<br></div></div></div></div>
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