From owner-chemistry@ccl.net Fri Nov 6 05:58:01 2015 From: "Jan Goetze jpg9=-=st-andrews.ac.uk" To: CCL Subject: CCL:G: ONIOM calculations in Gaussian Message-Id: <-51861-151106055619-1725-3kM/pz5UP4wgxvIMYxTJwA::server.ccl.net> X-Original-From: Jan Goetze Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_HE1PR06MB14845E2E431CFF03359D907AF0280HE1PR06MB1484eurp_" Date: Fri, 6 Nov 2015 10:55:51 +0000 MIME-Version: 1.0 Sent to CCL by: Jan Goetze [jpg9[A]st-andrews.ac.uk] --_000_HE1PR06MB14845E2E431CFF03359D907AF0280HE1PR06MB1484eurp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Petra, we encountered a similar problem a few weeks ago. I appears that Gaussian09= does sometimes automatically create link atoms or checks for atoms that sh= ould be replaced by link atoms (although the online manual explicitly state= s that it does not do that: "Note: All link atoms must be specified by the = user. Gaussian 09 does not define them automatically or provide any default= s."). A possible workaround might be using GaussView to set up the system. In the case of diamond, however, since you probably require multivalent lin= k atoms (i.e., one link atom bound to two or more border carbons), you migh= t need to resort to more advanced schemes than simple hydrogen saturation. = Just visualise your problematic model, the coordinates are given in the log= file. You should be able to see where the problem comes from. Cheers, Jan > > Sent to CCL by: "Petra Matunova" [petra.matunova]|[seznam.cz] > The surface is hydrogen-terminated and there where should be a > continuation to the bulk are hydrogens too (it is a corner of a > nanoparticle). > > >> "zborowsk zborowsk[a]chemia.uj.edu.pl" wrote: >> >> Sent to CCL by: zborowsk [zborowsk%chemia.uj.edu.pl] >> >> I must say I am a bit suprised by presence of hydrogen in your >> diamond.... >> >> >> W dniu 2015-11-04 12:06, Petra Matunova petra.matunova]![seznam.cz >> napisa(a): >> > Sent to CCL by: "Petra Matunova" [petra.matunova%%seznam.cz] >> > I am performing an ONIOM optimization calculation of a diamond >> > nanoparticle, using b3lyp/6-31g(d):b3lyp/3-21g method. The system >> > contains 206 C atoms and 130 H atoms in the high level and 488 C >> > atoms >> > 188 H atoms in the low level. When I set the charge and multiplicity >> > as following: 0 1 0 1 0 1, the system do the low level SCF >> > calculation >> > without problems, but when starts with the high level calculation on >> > the model system, it ends with error: >> > >> > The combination of multiplicity 1 and 1455 electrons is impossible. >> > >> > It only works when I set 0 1 0 2 0 2. In the high level system there >> > are 1366 electrons plus 89 link electrons from H atoms used as link >> > atoms. >> > >> > I had a problem with the specification of the link atoms on the >> > boundary between the low level and high level system. The low level C >> > atom close to the boundary has two bonds to another 2 high level C >> > atoms. I haven't known how to deal with that, as far as I know >> > Gaussian allows to specify only one bond to for every low level atom >> > to a high level atom. So I specified for the low level C atom linked >> > to 2 high level C atoms only one link H atom and set the >> > corresponding >> > scale factor to 1, e.g.: >> > >> > C -1 3.953927 3.329465 3.558583 L H 18 1. >> > >> > Like this, I got only a following warning in output, e.g.: >> > >> > WARNING: Link atom host 21 is close to both atoms 18 and 123. >> > Should it be oligovalent? >> > >> > Is there a way how to specify a link of the low level C to both of >> > the high level C to which it is bonded? Or how to solve that, would >> > it >> > be right to leave the multiplicity to one? >> > >> > Thank you for your help! >> > Best regards, >> > Petra >> > >> > >> > >> > -=3D This is automatically added to each message by the mailing script >> > =3D- >> > To recover the email address of the author of the message, please >> > change> Conferences: >> > http://server.ccl.net/chemistry/announcements/conferences/-- >> https://www.youtube.com/watch?v=3DIGyfx3Pmeyk >> Krzysztof K. Zborowski >> Faculty of Chemistry >> Jagiellonian University >> 3 Ingardena Street >> 30-060 Krakow >> Poland >> phone: +48(12)663-2067 >> email: zborowsk]~[chemia.uj.edu.pl >> gg 3817259 >> skype kzys70 >> www.chemia.uj.edu.pl/~zborowsk >> >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > Jan Philipp G=F6tze School of Chemistry University of St Andrews North Haugh St Andrews, Fife KY16 9ST, Scotland, United Kingdom Tel.: +44 (0)1334-464748 (ext. 14141) --_000_HE1PR06MB14845E2E431CFF03359D907AF0280HE1PR06MB1484eurp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Petra,

we encountered a similar problem a few weeks ago. I appears that Gaussia= n09 does sometimes automatically create link atoms or checks for atoms that= should be replaced by link atoms (although the online manual explicitly st= ates that it does not do that: "Note: All link atoms must be specified by the user. Gaussian 09 does not define = them automatically or provide any defaults."). A possible workaround m= ight be using GaussView to set up the system.


In the case of diamond, however, since you probably require multivalent = link atoms (i.e., one link atom bound to two or more border carbons), you m= ight need to resort to more advanced schemes than simple hydrogen saturatio= n. Just visualise your problematic model, the coordinates are given in the log file. You should be able to se= e where the problem comes from.


Cheers,

Jan


>
> Sent to CCL by: "Petra  Matunova" [petra.matunova]|[sez= nam.cz]
> The surface is hydrogen-terminated and there where should be a
> continuation to the bulk are hydrogens too (it is a corner of a
> nanoparticle).
>
>
>> "zborowsk zborowsk[a]chemia.uj.edu.pl"  wrote:
>>
>> Sent to CCL by: zborowsk [zborowsk%chemia.uj.edu.pl]
>>
>> I must say I am a bit suprised by presence of hydrogen in your
>> diamond....
>>
>>
>> W dniu 2015-11-04 12:06, Petra Matunova petra.matunova]![seznam.cz=
>> napisa(a):
>> > Sent to CCL by: "Petra  Matunova" [petra.matun= ova%%seznam.cz]
>> > I am performing an ONIOM optimization calculation of a diamon= d
>> > nanoparticle, using b3lyp/6-31g(d):b3lyp/3-21g method. The sy= stem
>> > contains 206 C atoms and 130 H atoms in the high level and 48= 8 C
>> > atoms
>> > 188 H atoms in the low level. When I set the charge and multi= plicity
>> > as following: 0 1 0 1 0 1, the system do the low level SCF >> > calculation
>> > without problems, but when starts with the  high level c= alculation on
>> > the model system, it ends with error:
>> >
>> > The combination of multiplicity 1 and  1455 electrons is= impossible.
>> >
>> > It only works when I set  0 1 0 2 0 2. In the high level= system there
>> > are 1366 electrons plus 89 link electrons from H atoms used a= s link
>> > atoms.
>> >
>> > I had a problem with the specification of the link atoms on t= he
>> > boundary between the low level and high level system. The low= level C
>> > atom close to the boundary  has two bonds to another 2 h= igh level C
>> > atoms. I haven't known how to deal with that, as far as I kno= w
>> > Gaussian allows to specify only one bond to for every low lev= el atom
>> > to a high level atom. So I specified for the low level C atom= linked
>> > to 2 high level C atoms only one link H atom and set the
>> > corresponding
>> > scale factor to 1, e.g.:
>> >
>> >  C      -1   &nb= sp; 3.953927    3.329465    3.558583 L H 18&n= bsp; 1.
>> >
>> > Like this, I got only a following warning in output, e.g.: >> >
>> > WARNING: Link atom host   21 is close to both atoms= 18 and  123.
>> > Should it be oligovalent?
>> >
>> > Is there a way how to specify a link of the low level C to bo= th of
>> > the high level C to which it is bonded? Or how to solve that,= would
>> > it
>> > be right to leave the multiplicity to one?
>> >
>> > Thank you for your help!
>> > Best regards,
>> > Petra
>> >
>> >
>> >
>> > -=3D This is automatically added to each message by the maili= ng script
>> > =3D-
>> > To recover the email address of the author of the message, pl= ease
>> > change> Conferences:
>> > http://server.ccl.net/chemistry/announcements/conferences/--<= br> >> https://www.youtube.com/watch?v=3DIGyfx3Pmeyk
>> Krzysztof K. Zborowski
>> Faculty of Chemistry
>> Jagiellonian University
>> 3 Ingardena Street
>> 30-060 Krakow
>> Poland
>> phone: +48(12)663-2067
>> email: zborowsk]~[chemia.uj.edu.pl
>> gg 3817259
>> skype kzys70
>> www.chemia.uj.edu.pl/~zborowsk
>>
>>
>
>
>
> -=3D This is automatically added to each message by the mailing script= =3D-
> To recover the email address of the author of the message, please chan= ge
>
>
>
>
>       http://www.ccl.net/cgi-bin/ccl/sen= d_ccl_message
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>
> >
>
>       >
>
>
>
>


Jan Philipp G=F6tze
School of Chemistry
University of St Andrews
North Haugh
St Andrews, Fife
KY16 9ST, Scotland, United Kingdom

Tel.: +44 (0)1334-464748 (ext. 14141)
--_000_HE1PR06MB14845E2E431CFF03359D907AF0280HE1PR06MB1484eurp_-- From owner-chemistry@ccl.net Fri Nov 6 08:25:01 2015 From: "Larissa Schneider lalasch#%#gmail.com" To: CCL Subject: CCL: Charmm22 force field parameters for phophorylated serine in Tinker Message-Id: <-51862-151105144608-6760-hnIkpUqygxwW/i6XGG5qGg|a|server.ccl.net> X-Original-From: "Larissa Schneider" Date: Thu, 5 Nov 2015 14:46:06 -0500 Sent to CCL by: "Larissa Schneider" [lalasch||gmail.com] Dear all, I'm looking for some way to find the global minimum of a peptide with a phosphorylated serine. Until now I was working with non-phosphorylated peptides, then, I was using Tinker's Monte Carlo algorithm with the Charmm22 force field. When I started to work with the phosphorylated one, I noticed that there wasn't the paramaters for this aminoacid. Where can I find this parameters or what other way can I use to find the global minimum of a phosphorylated peptide using the Charmm force field? Thank you, Larissa Schneider From owner-chemistry@ccl.net Fri Nov 6 09:53:01 2015 From: "Jim Kress jimkress35 . gmail.com" To: CCL Subject: CCL: Charmm22 force field parameters for phophorylated serine in Tinker Message-Id: <-51863-151106094609-6301-oXcxw6TW29Hpa6HCeTHAWA\a/server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Nov 2015 09:45:48 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35*_*gmail.com] Have you tried to generate the parameters using the ffTK plugin for VMD? The Force Field Toolkit is comprised of a set of tools that aid users in the development of CHARMM-compatible forcefield parameters, including charges, bonds, angles, and dihedrals. These tools are accessed through the provided GUI, which greatly simplifies the setup and analysis of the underlying calculations http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/ Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com_._ccl.net [mailto:owner-chemistry+jimkress35==gmail.com_._ccl.net] On Behalf Of Larissa Schneider lalasch#%#gmail.com Sent: Thursday, November 05, 2015 2:46 PM To: Kress, Jim Subject: CCL: Charmm22 force field parameters for phophorylated serine in Tinker Sent to CCL by: "Larissa Schneider" [lalasch||gmail.com] Dear all, I'm looking for some way to find the global minimum of a peptide with a phosphorylated serine. Until now I was working with non-phosphorylated peptides, then, I was using Tinker's Monte Carlo algorithm with the Charmm22 force field. When I started to work with the phosphorylated one, I noticed that there wasn't the paramaters for this aminoacid. Where can I find this parameters or what other way can I use to find the global minimum of a phosphorylated peptide using the Charmm force field? Thank you, Larissa Schneiderhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 6 10:43:01 2015 From: "Demian Riccardi demianriccardi#gmail.com" To: CCL Subject: CCL: Charmm22 force field parameters for phophorylated serine in Tinker Message-Id: <-51864-151106100435-14199-SESJElj9hfEjHMejwvoi2A[]server.ccl.net> X-Original-From: Demian Riccardi Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 6 Nov 2015 10:04:28 -0500 Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2104\)) Sent to CCL by: Demian Riccardi [demianriccardi() gmail.com] I think you can do phosphorylation via CHARMM-GUI http://www.charmm-gui.org > On Nov 5, 2015, at 2:46 PM, Larissa Schneider lalasch#%#gmail.com wrote: > > > Sent to CCL by: "Larissa Schneider" [lalasch||gmail.com] > Dear all, > > I'm looking for some way to find the global minimum of a peptide with a > phosphorylated serine. Until now I was working with non-phosphorylated > peptides, then, I was using Tinker's Monte Carlo algorithm with the > Charmm22 force field. When I started to work with the phosphorylated one, I > noticed that there wasn't the paramaters for this aminoacid. > > Where can I find this parameters or what other way can I use to find the > global minimum of a phosphorylated peptide using the Charmm force field? > > Thank you, > Larissa Schneider> > From owner-chemistry@ccl.net Fri Nov 6 18:39:00 2015 From: "Phil Hasnip phil.hasnip_-_york.ac.uk" To: CCL Subject: CCL: Materials Studio GUI Message-Id: <-51865-151106182602-15115-hkt1vp8GKYT0J56TLz5UMg _ server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary=089e01227efc73b0a20523e776aa Date: Fri, 6 Nov 2015 23:18:35 +0000 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip()york.ac.uk] --089e01227efc73b0a20523e776aa Content-Type: text/plain; charset=UTF-8 Dear Dan, I develop the CASTEP ab initio program for which Materials Studio has a module and interface, so although I don't have all that much experience with Materials Studio I do know a little about how it works and I'll answer as best I can. The term "Materials Studio" refers to the GUI developed by BIOVIA which, as you rightly point out, only runs on Windows. It is designed with a client-server architecture, so the GUI communicates with "server" codes which do the actual simulations; BIOVIA do ship many of these server codes for Linux as well as Windows, and I presume it's these that you've installed on your cluster. You can run the GUI on a PC under Windows, and set-up, run and analyse the "server" calculations on your cluster from this GUI. You can also use it to just write out input files for you to copy manually to a remote machine, and if you copy the output files back you can analyse and visualise them in Materials Studio. You don't necessarily have to have a physical Windows machine; I have successfully installed and run Materials Studio on a virtual machine (vmplayer) with various Windows versions. This is the only way I know of to run the Materials Studio GUI under Linux (or, indeed, MacOS X). If you really don't want to use Materials Studio to set up calculations, I'd be surprised if you couldn't find on-line examples of how to set up input files manually. Perhaps if you tell us which server codes you're interested in we could provide more specific help? For visualising results > from quantum chemistry codes you might like to investigate jmol or xcrysden (both free); there are many other options, but these are the ones I've used personally. For analysis of DOS and spectra there's always Optados, which is also free, though depending on which server code you're using you might need to write a small interface code. For CASTEP-specific advice on setting up simulations: 1. You'll find lots of non-Materials Studio examples at www.castep.org 2. You can always use "castep.mpi --help search " to pull out all the CASTEP keywords whose descriptions match "", or "castep.mpi --help " to get the detailed description of input keyword "". 3. The Materials Studio help is pretty good for documenting keywords and input files, is searchable, and has tutorial and example calculations as well with output as well as input. That's the best I can do without knowing more about your set-up. Hope it helps! All the best, Phil Hasnip ----------------------------------------------------------------------------- Dr Phil Hasnip Email: phil.hasnip],[york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 324624 York YO10 5DD On 29 October 2015 at 22:53, Dan Pope daniel.j.pope(!)wsu.edu < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: "Dan Pope" [daniel.j.pope-.-wsu.edu] > I am new to using Materials Studio, which we recently compiled on our > Rocks Linux cluster. All of the examples I am finding appear to utilize a > GUI from Windows. Can anyone tell me - does Materials Studio 8.0, or any of > its modules, have a GUI that is executable from a Linux command prompt? If > so where is its location? > > Regards, > Dan Pope> > > --089e01227efc73b0a20523e776aa Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Dan,

I develop the C= ASTEP ab=20 initio program for which Materials Studio has a module and interface, so although I don't have all that much experience with Materials Studio I= =20 do know a little about how it works and I'll answer as best I can.
<= /div>

The term "Materials Studio" refers to the GUI developed by BIOVIA wh= ich, as you rightly point out, only runs on Windows. It is designed with a=20 client-server architecture, so the GUI communicates with "server"= codes=20 which do the actual simulations; BIOVIA do ship many of these server=20 codes for Linux as well as Windows, and I presume it's these that you&#= 39;ve installed on your cluster. You can run the GUI on a PC under Windows,=20 and set-up, run and analyse the "server" calculations on your clu= ster=20 > from this GUI. You can also use it to just write out input files for you to copy manually to a remote machine, and if you copy the output files bac= k you can analyse and visualise them in Materials Studio.

You don= 9;t necessarily have to have a physical Windows machine; I have successfully installed and=20 run Materials Studio on a virtual machine (vmplayer) with various=20 Windows versions. This is the only way I know of to run the Materials=20 Studio GUI under Linux (or, indeed, MacOS X).

If you really don't want to use Materials Studio to set up calculations, I'd be= =20 surprised if you couldn't find on-line examples of how to set up input= =20 files manually. Perhaps if you tell us which server codes you're=20 interested in we could provide more specific help? For visualising results = > from quantum chemistry codes you might like to investigate jmol=20 or xcrysden (both free); there are many other options, but these are the ones I've used personally. For analysis of DOS and spectra there's= =20 always Optados, which is also free, though depending on which server=20 code you're using you might need to write a small interface code.
For CASTEP-specific advice on setting up simulations:

1. You'l= l find lots of non-Materials Studio examples at www.castep.org

2. You can always use &q= uot;castep.mpi --help search <text>" to pull out=20 all the CASTEP keywords whose descriptions match "<text>", = or "castep.mpi --help <keyword>" to get the detailed description of input=20 keyword "<keyword>".

3. The Materials Studio help is= pretty good for documenting keywords and input files, is searchable, and has=20 tutorial and example calculations as well with output as well as input.
That's the best I can do without knowing more about you= r set-up. Hope it helps!

All the best,

Phil Hasnip

--------------------------------------------------------------------= ---------
Dr Phil Hasnip =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Email:= phil.hasnip],[yo= rk.ac.uk
Dept of Physics
University of York =C2=A0 =C2=A0 =C2=A0 = =C2=A0Tel: =C2=A0+44 (0)1904 324624
York YO10 5DD

On 29 October 2015 at 22:53, Dan Pope daniel= .j.pope(!)wsu.edu <owner-chemistry],[cc= l.net> wrote:

Sent to CCL by: "Dan=C2=A0 Pope" [daniel.j.pope-.-wsu.edu]
I am new to using Materials Studio, which we recently compiled on our Rocks= Linux cluster. All of the examples I am finding appear to utilize a GUI fr= om Windows. Can anyone tell me - does Materials Studio 8.0, or any of its m= odules, have a GUI that is executable from a Linux command prompt? If so=C2= =A0 where is its location?

Regards,
Dan Pope



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