From owner-chemistry@ccl.net Tue Oct 23 00:49:00 2018 From: "Clayton Spencer cfspence ~~ ic.edu" To: CCL Subject: CCL: Doing ONIOM QM/MM calculations on biomolecules Message-Id: <-53524-181023004013-23994-lTsMYQoAM2VKBrgMBTZFdw++server.ccl.net> X-Original-From: "Clayton Spencer" Date: Tue, 23 Oct 2018 00:40:12 -0400 Sent to CCL by: "Clayton Spencer" [cfspence]~[ic.edu] I'd like to learn the practical aspects of doing ONIOM QM/MM on biomolecules and have two questions. 1. What are some good resources for learning the practical aspects about how to do such computations? 2. One initial resource that I have looked at is the ONIOM section of Chapter 9 of _Exploring Chemistry with Electronic Structure Methods_, 3rd ed, by Foresman and Frisch. My question: are there free/open source alternatives to GaussView software for academic institutions for doing some of the QM/MM related tasks on biomolecules starting from the pdb structure? Some of the indicated tasks include: removing water molecules from the pdb file, removing duplicate protein copies from a pdb file, adding missing residues to the pdb file, specifying the ONIOM layers, etc. Thanks, in advance, for pointing me in the right direction. From owner-chemistry@ccl.net Tue Oct 23 02:40:00 2018 From: "Kantnerova, Kristyna Kristyna.Kantnerova===empa.ch" To: CCL Subject: CCL: Doing ONIOM QM/MM calculations on biomolecules Message-Id: <-53525-181023023749-10331-y7RRrB6irzJRTz0gRQ3fhg/a\server.ccl.net> X-Original-From: "Kantnerova, Kristyna" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 23 Oct 2018 06:37:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Kantnerova, Kristyna" [Kristyna.Kantnerova(a)empa.ch] Hi Clayton, you can check out the molUP plugin for the VMD software. https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.25189 It is pretty easy to use for preparation of the pdf file for the actual ONIOM calculation. For preparation of the pdb file, I was just using AmberTools, you can find many tutorials online. Cheers, Kristýna > -----Original Message----- > From: owner-chemistry+kristyna.kantnerova==empa.ch++ccl.net [mailto:owner- > chemistry+kristyna.kantnerova==empa.ch++ccl.net] On Behalf Of Clayton > Spencer cfspence ~~ ic.edu > Sent: 23 October 2018 06:40 > To: Kantnerova, Kristyna > Subject: CCL: Doing ONIOM QM/MM calculations on biomolecules > > > Sent to CCL by: "Clayton Spencer" [cfspence]~[ic.edu] > I'd like to learn the practical aspects of doing ONIOM QM/MM on > biomolecules > and have two questions. > > 1. What are some good resources for learning the practical aspects about how > to do such computations? > > 2. One initial resource that I have looked at is the ONIOM section of Chapter > 9 of _Exploring Chemistry with Electronic Structure Methods_, 3rd ed, by > Foresman and Frisch. My question: are there free/open source alternatives to > GaussView software for academic institutions for doing some of the QM/MM > related tasks on biomolecules starting from the pdb structure? Some of the > indicated tasks include: removing water molecules from the pdb file, removing > duplicate protein copies from a pdb file, adding missing residues to the pdb > file, specifying the ONIOM layers, etc. > > Thanks, in advance, for pointing me in the right direction.> From owner-chemistry@ccl.net Tue Oct 23 03:23:00 2018 From: "Christoph Riplinger riplinger~~faccts.de" To: CCL Subject: CCL: Doing ONIOM QM/MM calculations on biomolecules Message-Id: <-53526-181023032011-27963-QbIP05BmHv3d0GUUqYqaew,,server.ccl.net> X-Original-From: Christoph Riplinger Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 23 Oct 2018 09:20:02 +0200 MIME-Version: 1.0 Sent to CCL by: Christoph Riplinger [riplinger^_^faccts.de] Dear Clayton, Regarding your second question: VMD can be used to prepare hybrid QM/MM calculations which can then be carried out with NAMD and ORCA. VMD contains the easy-to-use QwikMD module, which enables you to prepare such a calculation in short time. VMD, NAMD and ORCA are free for academic usage. You can check out our recent paper for a more detailed description of the ORCA/NAMD QM/MM setup: https://www.nature.com/articles/nmeth.4638 Best regards, Christoph On 23.10.18 06:40, Clayton Spencer cfspence ~~ ic.edu wrote: > Sent to CCL by: "Clayton Spencer" [cfspence]~[ic.edu] > I'd like to learn the practical aspects of doing ONIOM QM/MM on biomolecules > and have two questions. > > 1. What are some good resources for learning the practical aspects about how > to do such computations? > > 2. One initial resource that I have looked at is the ONIOM section of Chapter > 9 of _Exploring Chemistry with Electronic Structure Methods_, 3rd ed, by > Foresman and Frisch. My question: are there free/open source alternatives to > GaussView software for academic institutions for doing some of the QM/MM > related tasks on biomolecules starting from the pdb structure? Some of the > indicated tasks include: removing water molecules from the pdb file, removing > duplicate protein copies from a pdb file, adding missing residues to the pdb > file, specifying the ONIOM layers, etc. > > Thanks, in advance, for pointing me in the right direction.> > -- FAccTs GmbH Rolandstrasse 67, 50677 Köln Amtsgericht Köln HRB 88406 Geschäftsführer: Dr. Christoph Riplinger https://www.faccts.de From owner-chemistry@ccl.net Tue Oct 23 03:57:01 2018 From: "Arthur Zalevsky aozalevsky%a%gmail.com" To: CCL Subject: CCL: Doing ONIOM QM/MM calculations on biomolecules Message-Id: <-53527-181023032607-31310-mbGFjxCMcJOnxvsmN4mOFQ##server.ccl.net> X-Original-From: Arthur Zalevsky Content-Type: multipart/alternative; boundary="000000000000100b380578e04887" Date: Tue, 23 Oct 2018 10:25:47 +0300 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky__gmail.com] --000000000000100b380578e04887 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Dr. Spencer, it's nice to see how our QM/MM is growing. We use Gromacs/DFTB and in-house version of Gromacs/MOPAC2012 for QM/MM metadynamics calculations. For example, check https://www.ncbi.nlm.nih.gov/pubmed/27774510 and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085465/ Due to the lack of robust instruments, we had to develop (or at least heavy modify available tools) our own tools for quality control of structures (water molecules can be extremely tricky and important, especially for enzymes) of preparation of input files (topology files for ligands, selection of quantum systems, generation of topology and index files). Those instruments still in beta stage but I hope to discuss those tools during the forthcoming GROMACS workshop (https://baltichpc.org/) and to make them publicly available as soon as possible. Regards, Arthur -- Ph.D. student Virtual Structural Biology Group Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University email: aozalevsky+*+fbb.msu.ru email: aozalevsky+*+gmail.com web: https://vsb.fbb.msu.ru cell: +79268299066 =D0=B2=D1=82, 23 =D0=BE=D0=BA=D1=82. 2018 =D0=B3. =D0=B2 9:58, Clayton Spen= cer cfspence ~~ ic.edu < owner-chemistry+*+ccl.net>: > > Sent to CCL by: "Clayton Spencer" [cfspence]~[ic.edu] > I'd like to learn the practical aspects of doing ONIOM QM/MM on > biomolecules > and have two questions. > > 1. What are some good resources for learning the practical aspects about > how > to do such computations? > > 2. One initial resource that I have looked at is the ONIOM section of > Chapter > 9 of _Exploring Chemistry with Electronic Structure Methods_, 3rd ed, by > Foresman and Frisch. My question: are there free/open source alternative= s > to > GaussView software for academic institutions for doing some of the QM/MM > related tasks on biomolecules starting from the pdb structure? Some of > the > indicated tasks include: removing water molecules from the pdb file, > removing > duplicate protein copies from a pdb file, adding missing residues to the > pdb > file, specifying the ONIOM layers, etc. > > Thanks, in advance, for pointing me in the right direction. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000000000000100b380578e04887 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Dr. Spencer,

it's nice to see how our QM/= MM is growing.=C2=A0

We use Gromacs/DFTB and in-house ve= rsion of Gromacs/MOPAC2012 for QM/MM metadynamics calculations. For example= , check=C2=A0https= ://www.ncbi.nlm.nih.gov/pubmed/27774510=C2=A0and=C2=A0https://www.ncbi.nlm.nih.g= ov/pmc/articles/PMC6085465/=C2=A0

Due to the lack of robust=C2= =A0instruments, we had to develop (or at least heavy modify available=C2=A0= tools) our own tools for quality control of structures (water molecules can= be extremely=C2=A0tricky and important, especially for enzymes) of prepara= tion of input files (topology files for ligands, selection of quantum syste= ms, generation of topology and index files).=C2=A0

Those instruments= still in beta stage but I hope to discuss those tools during the forthcomi= ng GROMACS workshop (https://baltichpc.o= rg/) and to make them publicly available as soon as possible.

Re= gards,
Arthur

--
Ph.D. student
Virtual Structural Biology G= roup
Faculty of Bioengineering and Bioinformatics
Lomonosov Moscow St= ate University

email: aozalevsky+*+fbb.msu.ru
email: a= ozalevsky+*+gmail.com
web: https:/= /vsb.fbb.msu.ru
cell: +79268299066



=D0=B2=D1=82, 23 =D0=BE=D0=BA=D1=82. 2018 =D0=B3.= =D0=B2 9:58, Clayton Spencer cfspence ~~ ic.edu<= /a> <owner-chemistry+*+ccl.net<= /a>>:

Sent to CCL by: "Clayton=C2=A0 Spencer" [cfspence]~[ic.edu]
I'd like to learn the practical aspects of doing ONIOM QM/MM on biomole= cules
and have two questions.

1. What are some good resources for learning the practical aspects about ho= w
to do such computations?

2. One initial resource that I have looked at is the ONIOM section of Chapt= er
9 of _Exploring Chemistry with Electronic Structure Methods_, 3rd ed, by Foresman and Frisch.=C2=A0 My question: are there free/open source alternat= ives to
GaussView software for academic institutions for doing some of the QM/MM related tasks on biomolecules starting from the pdb structure?=C2=A0 Some o= f the
indicated tasks include: removing water molecules from the pdb file, removi= ng
duplicate protein copies from a pdb file, adding missing residues to the pd= b
file, specifying the ONIOM layers, etc.

Thanks, in advance, for pointing me in the right direction.



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