From owner-chemistry@ccl.net Fri Dec 22 01:33:01 2017 From: "Rinsha CH rinsha_p170030cy%%nitc.ac.in" To: CCL Subject: CCL:G: Error while optimizing protien in Gaussian09 using Amber force field Message-Id: <-53116-171222002951-27043-uP6aqdJraeWRpjFrLF0hqg+/-server.ccl.net> X-Original-From: "Rinsha CH" Date: Fri, 22 Dec 2017 00:29:49 -0500 Sent to CCL by: "Rinsha CH" [rinsha_p170030cy]^[nitc.ac.in] Hello, I was optimizing the structure of a protein in gaussian09 using amber force field (ff12sb) and I encountered with an error, 1)Read MM parameter file: ff12SB IFunc= -1 Function name not recognized in RdPar Error termination via Lnk1e in /nfs-scratch/Apps/gaussian09/g09/l101.exe 2) Read MM parameter file: Wrong or no center in RdPar. Error termination via Lnk1e in /nfs-scratch/Apps/gaussian09/g09/l101.exe How can I solve these error? Thanks in advance. From owner-chemistry@ccl.net Fri Dec 22 07:57:00 2017 From: "Zeljko Vitnik zvitnik[-]chem.bg.ac.rs" To: CCL Subject: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian Message-Id: <-53117-171222075439-7801-uLwSx55in7VRJyj0eg7BSA/a\server.ccl.net> X-Original-From: Zeljko Vitnik Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 22 Dec 2017 13:54:28 +0100 MIME-Version: 1.0 Sent to CCL by: Zeljko Vitnik [zvitnik[]chem.bg.ac.rs] Hello Grigoriy, In your case, I would first adapt the geometry. I would put Cartesians part on the front of list and Z-Matrix part will be defined on the three atoms from Cartesians part. This will at the same time cancel the need for Dummy atom and prevents movement of large Cartesians part due to small changes in geometry parameters of Z-Matrix part. Next, Gaussian 09 has the option for freezing the any part of geometry on the basis of provided list. See OPT=ReadFreeze option. It must be followed by the list of frozen atoms after the geometry list. It must be separated by one empty line and in a form of: atoms=list [notatoms=list], where each list is a comma or space-separated list of atom numbers, atom number ranges and/or atom types after the geometry list separated with one separated by one empty line. I think that this option can be combined with ModRedundant option, too. This allows you to do the simply scan of any parameter defined in Z-Matrix part. If you must to use Dummy atom, use Bq instead of X. Greeting, Z Vitnik On 2017-12-18 15:34, Grigoriy Zhurko reg_zhurko||chemcraftprog.com wrote: > Sent to CCL by: Grigoriy Zhurko [reg_zhurko]~[chemcraftprog.com] > Hello, > > I need to perform a PES scan in Gaussian, so that the distance > between an atom and the center between two other atoms will be > scanned. > When I need to simply scan an iteratomic distance, I use > OPT(MODREDUNDANT). But in current case I have to use a z-matrix and > add a dummy atom (the center between two real atoms). > It is possible to use only Z-matrix for this job, but the result > becomes rather bad: the optimization starts with evident bugs > (probably because this geometry has rings). > I tried to combine the Z-matrix with the Cartesians. I created the > following input file: > > %NPROCSHARED=3 > #P uwB97XD/6-31G(D,P) OPT(Z-Matrix,LOOSE) > NOSYMM > > Silicon > > 0 1 > X > N 1 R12 > X 1 1.400000 2 90.000000 > N 1 R12 3 90.000000 2 180.000000 > N 1 R15 2 A215 3 -90.000000 > N 1 R16 3 A316 5 D5316 > Zn 1 R17 2 A217 5 -D5217 > 6 0.000000000 2.863016000 1.101006000 > 6 0.000000000 2.425840000 2.425840000 > 6 0.000000000 1.101006000 2.863016000 > 1 0.000000000 3.193595000 3.193595000 > 6 0.000000000 2.863016000 -1.101006000 > 6 0.000000000 2.425840000 -2.425840000 > 6 0.000000000 1.101006000 -2.863016000 > 1 0.000000000 3.193595000 -3.193595000 > 6 0.000000000 -1.101006000 -2.863016000 > 6 0.000000000 -2.425840000 -2.425840000 > 6 0.000000000 -2.863016000 -1.101006000 > 1 0.000000000 -3.193595000 -3.193595000 > 6 0.000000000 -2.863016000 1.101006000 > 6 0.000000000 -2.425840000 2.425840000 > 6 0.000000000 -1.101006000 2.863016000 > 1 0.000000000 -3.193595000 3.193595000 > 6 0.000000000 -4.245855000 0.681548000 > 6 0.000000000 -4.245855000 -0.681548000 > 6 0.000000000 -0.681548000 -4.245855000 > 6 0.000000000 0.681548000 -4.245855000 > 6 0.000000000 -0.681548000 4.245855000 > 6 0.000000000 0.681548000 4.245855000 > 6 0.000000000 4.245855000 0.681548000 > 6 0.000000000 4.245855000 -0.681548000 > 1 0.000000000 -5.096481000 1.350466000 > 1 0.000000000 -5.096481000 -1.350466000 > 1 0.000000000 -1.350466000 -5.096481000 > 1 0.000000000 1.350466000 -5.096481000 > 1 0.000000000 5.096481000 -1.350466000 > 1 0.000000000 5.096481000 1.350466000 > 1 0.000000000 -1.350466000 5.096481000 > 1 0.000000000 1.350466000 5.096481000 > Variables: > R12 = 2.04198300 > R15 = 2.04198300 > A215 = 90.00000000 > R16 = 2.04198300 > A316 = 90.00000000 > D5316 = 180.00000000 > A217 = 90.00000000 > D5217 = 90.00000000 > constants > R17 = 0.40000000 s 20 0.2 > > This job constructs a valid geometry, the optimization starts, but it > starts incorrectly: during the optimization, only the Z-matrix > parameters are varied, while the coordinates of most atoms are fixed. > Can I do something to make Gaussian optimize these atomic coordinates > as well? > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/-- ************************************************************ Dr Željko Vitnik Senior research associate IChTM-Department of Chemistry, University of Belgrade Studentski trg 12-16, 11000 Belgrade (Serbia) Phone: (+381) 11-3336-735; Mobile: (+381) 64-1272-051 E-mail: zvitnik:_:chem.bg.ac.rs ************************************************************ From owner-chemistry@ccl.net Fri Dec 22 09:49:00 2017 From: "Andreas Klamt klamt{:}cosmologic.de" To: CCL Subject: CCL: 5th COSMO-RS symposium in March in Cologne Message-Id: <-53118-171222013652-9750-0jQM4ehdDXeser4JGbjJzw+*+server.ccl.net> X-Original-From: Andreas Klamt Content-Language: de-DE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 22 Dec 2017 07:36:43 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt!^!cosmologic.de] Dear computational chemistry colleagues, since Tymofii asked for more interesting conference announcements, let me invite all of you to our 5th COSMO-RS symposium in Cologne on March 6-8, 2018. (I hope that not all of you will come, since that would become a bit overcrowded.;-)) It will be a meeting of scientists from many areas of computational and experimental chemistry, ranging from chemical engineers, using COSMO-RS for predicting activity coefficients, environmental researchers, pharmaceutical modellers, fragrance and cosmetics experts, material and reaction simulation simulation people, and many more, all having in common, that accurate prediction of the solvent influence on the properties of their interest is crucial for their work. The meeting will combine presentations of applications by users, presentations of new improvements of the methods an extension of the applicability range, and discussions on future directions. As side events there will be introductions and training sessions for COSMO-RS newcomers. The meeting should be interesting for those who do - after more than 20 years after the COSMO-RS publication - still don't know the difference between COSMO and COSMO-RS, and for those, who like to see the current and future potential of this - currently most likely most predictive - solvation model. I will present there the COSMOplex method, an extension of COSMO-RS which allows for the efficient simulation of z-inhomogeneous self-organizing systems, as micelles, biomembranes, interfaces, liquid crystals, ..., requiring nothing else than COSMO files as input. It completely bypasses the need for force-fields or coarse-grained methods, is 100 times faster than MD simulations, and most likely more accurate. For more details and registrations see: http://www.cosmologic.de/symposium_2018.html With my best wishes for the Christmas holidays and the new year and hoping to see some of you in Cologne Andreas -- Join us at the 5th-COSMO-RS-Symposium March 2018 Details at www.cosmologic.de/symposium_2018.html -------------------------------------------------- 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