From owner-chemistry@ccl.net Tue Jun 20 04:05:01 2017 From: "Andreas Klamt klamt:+:cosmologic.de" To: CCL Subject: CCL:G: COSMO calculation results, how to interpret? Message-Id: <-52858-170619123537-17897-zMILTpvmv9mlYVcLy9F7tA^^^server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-15 Date: Mon, 19 Jun 2017 18:35:25 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt##cosmologic.de] Hi Sergey, in the COSMO files theinformationis written in the form - segment No, atom, element, coordinates of the segment center (in bohr units), chagre on the segment (in atomic units), area of the segment (in squared Angstrom, sorry for the inconsistency), then charge/area, and electrostatic potential at the center of the segment Please note that the polarization charge density should be averaged with a Gaussian width of 0.5 A in order to smooth the numerical noise resulting from the cavity segmentation. For details see the COSMO-RS papers. Best regards Andreas (father of COSMO) Am 19.06.2017 um 12:30 schrieb Sergey Sosnin sergey.sosnin]=[skolkovotech.ru: > Sent to CCL by: "Sergey Sosnin" [sergey.sosnin=-=skolkovotech.ru] > Hi, > > My target is to obtain a charged surface of a molecule using COSMO method. From my viewpoint, the results of COSMO calculations are the surfaces with charges. And polygons are used to represent surface in computer science. But the outputs of Mopac and Molpro don't look like a polygon mesh. > > For example, the output of Mopac: > > SEGMENT DATA: NPS= 1434 > NR. ATOM ELEM. COORDINATES (X, Y, Z) COSMO-CHARGE AREA SIGMA POTENTIAL > 1 1 8 1.124331 -0.200736 -0.123380 0.000322 0.055691 0.005774 -0.040056 > 2 1 8 0.896929 1.428347 0.330001 0.001065 0.159820 0.006663 -0.048840 > 3 1 8 1.743958 0.304266 1.465655 0.000823 0.159820 0.005151 -0.056846 > 4 1 8 2.329608 2.004282 1.271520 0.000391 0.159820 0.002448 -0.020262 > > It looks like, there are only points at the surface of the molecule. But if my assumption is right, what is the "area"? > > In principle, I can do triangulation to get the surface but how I can map the area and charge of each segment to my triangles?> > > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt]^[cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt