From owner-chemistry@ccl.net Wed Jun 16 05:21:00 2010 From: "Liu Jing jliu++cuhk.edu.hk" To: CCL Subject: CCL:G: TDDFT Message-Id: <-42121-100616051817-21939-o5dLekg51a8hy2VhuJ3v4A#%#server.ccl.net> X-Original-From: Liu Jing Content-Type: multipart/alternative; boundary=0016364d2b4b1c7d570489223305 Date: Wed, 16 Jun 2010 17:18:06 +0800 MIME-Version: 1.0 Sent to CCL by: Liu Jing [jliu-,-cuhk.edu.hk] --0016364d2b4b1c7d570489223305 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Dear Jim=A3=AC Thank you. I'v not used this program, maybe i should to take a deep look at it. Regards LIU,Jing 2010/6/15 Jim Kress ccl_nospam:_:kressworks.com > Have you tried ORCA? It is quite complete when it comes to calculations > involving virtually any kind of spectroscopy. > > > > http://www.thch.uni-bonn.de/tc/orca/ > > > > Jim Kress > > > > *From:* owner-chemistry+ccl_nospam=3D=3Dkressworks.com*o*ccl.net [mailto: > owner-chemistry+ccl_nospam =3D=3Dkressworks= .com > *o*ccl.net] *On Behalf Of *Liu Jing jliu]^[cuhk.edu.hk > *Sent:* Monday, June 14, 2010 9:38 PM > *To:* Kress, Jim > *Subject:* CCL:G: TDDFT > > > > Dear Jamin, > > Thank you for your quick reply. > > Would you like to say sth about the oscillator strengths. In my > > calculation this value is equal to zero for the first excited state, does > > it mean this transition is forbidden? > > > > Regards > > Liu, Jing > > 2010/6/15 Jamin Krinsky jamink()berkeley.edu > > Dear Jing, > > If you are using Gaussian, you cannot request excited-state multiplicitie= s > different from the ground state for open-shell molecules (the "singlets" = and > "triplets" options are ignored). You can of course calculate the > ground-state configuration for each multiplicity and compare energies of > those... Some other programs (Q-Chem included I think) will let you do > spin-flip TDDFT, but you'd want to read up on the subject before attempti= ng > it (I don't know much about it). > > Regards, > Jamin > > On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk < > owner-chemistry]~[ccl.net> wrote: > > Dear all, > > > > Can you tell me how to set the spin multiplicity of the excited states > when a open- > > shell system is concerned? > > > > Thank you and good luck. > > > > Yours Jing > > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink]~[berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > > --0016364d2b4b1c7d570489223305 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable
Dear Jim=A3=AC
  
   Thank you. I'v not used this program, maybe i should = to take
a deep look at it.
 
Regards
LIU,Jing

 
2010/6/15 Jim Kress ccl_nospam:_:kressworks.com = <owner-chem= istry.:.ccl.net>

Have= you tried ORCA?  It is quite complete when it comes to calculations i= nvolving virtually any kind of spectroscopy.

&nbs= p;

http://www.t= hch.uni-bonn.de/tc/orca/

&nbs= p;

Jim = Kress

&nbs= p;

From:<= span style=3D"FONT-SIZE: 10pt"> owner-chemistry+ccl_nospam=3D=3Dkressworks.com*o*ccl.net [mailto:owner-chemistry+ccl_nospam= =3D=3Dkressworks.com*o*ccl.net] On Behal= f Of Liu Jing jliu]^[= cuhk.edu.hk
Sent: Monday, June 14, 2010 9:38 PM
To: Kress, Jim
= Subject: CCL:G: TDDFT

 

Dear Jamin,

    Thank you for your quick reply.

    Would you like to say sth about t= he oscillator strengths. In my

calculation this value is equal to zero for the firs= t excited state, does

it mean this transition is forbidden?

 

Regards

Liu, Jing

2010/6/15 Jamin Krinsky jamink()berkeley.edu <owner-chemistry%ccl.net>

Dear Jing,

If y= ou are using Gaussian, you cannot request excited-state multiplicities diff= erent from the ground state for open-shell molecules (the "singlets&qu= ot; and "triplets" options are ignored). You can of course calcul= ate the ground-state configuration for each multiplicity and compare energi= es of those... Some other programs (Q-Chem included I think) will let you d= o spin-flip TDDFT, but you'd want to read up on the subject before atte= mpting it (I don't know much about it).

Regards,
Jamin

On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk <owner-chemistry]~[c= cl.net> wrote:

Dear all,

  

  Can you tell me how to set the spin mult= iplicity of the excited states when a open-

shell system is concerned?

 

 Thank you and good luck.

 

Yours Jing




--
Jamin L Krinsky, Ph.D.
Molecul= ar Graphics and Computation Facility
175 Tan Hall, University of Califor= nia, Berkeley, CA 94720
jamink]~[berkele= y.edu, 510-643-0616
http://glab.cchem.berkeley.edu

 


--0016364d2b4b1c7d570489223305-- From owner-chemistry@ccl.net Wed Jun 16 09:21:01 2010 From: "Iain Moal Iain.Moal{}cancer.org.uk" To: CCL Subject: CCL: Program for enzyme design Message-Id: <-42122-100616045757-19878-fuGZK7JBaxW/9fDBUWQrMg-,-server.ccl.net> X-Original-From: "Iain Moal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CB0D29.9B1358E5" Date: Wed, 16 Jun 2010 08:57:45 +0100 MIME-Version: 1.0 Sent to CCL by: "Iain Moal" [Iain.Moal[*]cancer.org.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01CB0D29.9B1358E5 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello WoA, The Baker group have managed to design an enzyme de novo, and much of thei= r code is available in their rosetta package (or its python implimentation= , pyrosetta). It might take a bit of work to get a small molecule into th= e package, but otherwise it should work quite well for your purpose. You = can optimise the position and orientation of the ligand, as well as the ba= ckbone conformation and the side-chain rotamers. When repacking the side-= chains, you can select certain residues and ask the program to search for = rotamers in all 20 amino acids, hence performing computational mutagenasis= on the fly. See workshop #6 on the PyRosetta website. Iain -----Original Message----- > From: owner-chemistry+iain.moal=3D=3Dcancer.org.uk(~)ccl.net on behalf of W = Agnessi witch.of.agnessi*gmail.com Sent: Tue 15/06/2010 21:38 To: Iain Moal Subject: CCL: Program for enzyme design =20 Sent to CCL by: "W Agnessi" [witch.of.agnessi[]gmail.com] Hello CCLers, I'm working on computational design of an enzyme to increase it's=20affini= ty for a non-natural substrate. I wish to mutate 2-3 residues at the ligan= d binding site such that it can bind better a non-natural substrate. Quite= a few X-ray structures are available for the apo as well as holo enzyme,w= ith different ligands. However no structure with that non-natural substrat= e is available. I'm looking for freely available softwares, which would be able to comput= ationally re-design the active site. My input to the program would be a (b= adly) docked structure of the enzyme and my ligand of interest. Any suggestions, comments, pointers, relevant literature links are most we= lcome. Thanks in advance -WoA -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cance= rresearchuk.org. We are a charity registered under number 1089464 and a co= mpany limited by guarantee registered in England & Wales under number 4325= 234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. O= ur central telephone number is 020 7242 0200. =20 This communication and any attachments contain information which is confid= ential and may also be privileged. It is for the exclusive use of the in= tended recipient(s). If you are not the intended recipient(s) please note= that any form of disclosure, distribution, copying or use of this communi= cation or the information in it or in any attachments is strictly prohibit= ed and may be unlawful. If you have received this communication in error,= please notify the sender and delete the email and destroy any copies of i= t. =20 E-mail communications cannot be guaranteed to be secure or error free, as = information could be intercepted, corrupted, amended, lost, destroyed, arr= ive late or incomplete, or contain viruses. We do not accept liability fo= r any such matters or their consequences. Anyone who communicates with us= by e-mail is taken to accept the risks in doing so. ------_=_NextPart_001_01CB0D29.9B1358E5-- From owner-chemistry@ccl.net Wed Jun 16 11:32:00 2010 From: "John Furr john.furr/./gmail.com" To: CCL Subject: CCL: Docking Software for Macrocycles Message-Id: <-42123-100616102116-16864-zDU53HmRoc2DGpL46zK8/A]|[server.ccl.net> X-Original-From: "John Furr" Date: Wed, 16 Jun 2010 10:21:15 -0400 Sent to CCL by: "John Furr" [john.furr|gmail.com] Hey gang, I'm looking for advise/tips about docking software that will work well with large macrocycles...19+ ring atoms. Software can be commercial or not. Currently we are using the Schrodinger suite of tools with moderate success. However our biggest limitation is that glide does not sample large ring conformations. This means that for every compounds we want to dock we have to first do an upfront conformational analysis and this takes several hours to do in a complete manner. To put it in units of time. It takes me about 4 hours per compound to get a docked pose for a single CPU. There are literally times that the chemistry team is faster than me! Obviously we are very interested in exploring other options that would allow us to improve our throughput without compromising robustness. So gang any advise and or tips? Cheers John Furr From owner-chemistry@ccl.net Wed Jun 16 12:52:00 2010 From: "Matthieu Montes matthieu.montes[]cnam.fr" To: CCL Subject: CCL: Program for enzyme design Message-Id: <-42124-100616104248-22199-L+DqsW5Sb4t/SpanzSKFmg**server.ccl.net> X-Original-From: Matthieu Montes Content-Type: multipart/alternative; boundary=Apple-Mail-2--109673659 Date: Wed, 16 Jun 2010 16:15:53 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Matthieu Montes [matthieu.montes+*+cnam.fr] --Apple-Mail-2--109673659 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed This paper may be of interest : Lopes A, Schmidt Am Busch M, Simonson T, .Computational design of =20 protein-ligand binding: modifying the specificity of asparaginyl-tRNA =20= synthetase. J Comput Chem. 2010 Apr 30;31(6):1273-86. Regards, Matthieu Montes Le 15 juin 10 =E0 22:38, W Agnessi witch.of.agnessi*gmail.com a =E9crit = : > > Sent to CCL by: "W Agnessi" [witch.of.agnessi[]gmail.com] > Hello CCLers, > > I'm working on computational design of an enzyme to increase it's =20 > affinity for a non-natural substrate. I wish to mutate 2-3 residues =20= > at the ligand binding site such that it can bind better a non-=20 > natural substrate. Quite a few X-ray structures are available for =20 > the apo as well as holo enzyme,with different ligands. However no =20 > structure with that non-natural substrate is available. > > I'm looking for freely available softwares, which would be able to =20= > computationally re-design the active site. My input to the program =20 > would be a (badly) docked structure of the enzyme and my ligand of =20 > interest. > > Any suggestions, comments, pointers, relevant literature links are =20 > most welcome. > > Thanks in advance > > -WoA > > > > -=3D This is automatically added to each message by the mailing =20 > script =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> > -- Matthieu Montes, PhD Ma=EEtre de Conf=E9rences / Assistant Professor Chaire de Bioinformatique Conservatoire National des Arts et M=E9tiers 292 Rue Saint-Martin 75003 Paris, France mailto:matthieu.montes[-]cnam.fr phone +33140272809 --Apple-Mail-2--109673659 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 This paper may be of interest = :




Sent to = CCL by: "W  Agnessi" = [witch.of.agnessi[]gmail.com]
Hello = CCLers,

I'm working on computational design of an enzyme to = increase it's affinity for a non-natural substrate. I wish to mutate 2-3 = residues at the ligand binding site such that it can bind better a = non-natural substrate. Quite a few X-ray structures are available for = the apo as well as holo enzyme,with different ligands. However no = structure with that non-natural substrate is available.

I'm = looking  for freely = available softwares, which would be able to computationally re-design = the active site. My input to the program would be a (badly) docked = structure of the enzyme and my ligand of interest.

Any = suggestions, comments, pointers, relevant literature links are most = welcome.

Thanks in advance




-=3D This is = automatically added to each message by the mailing script =3D-
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E-mail to administrators: CHEMISTRY-REQUEST[-]ccl.net = or use

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Matthieu Montes, = PhD
Ma=EEtre de Conf=E9rences / Assistant = Professor
Chaire de Bioinformatique
Conservatoire = National des Arts et M=E9tiers
292 Rue = Saint-Martin
75003 Paris, France
phone +33140272809


=
= --Apple-Mail-2--109673659-- From owner-chemistry@ccl.net Wed Jun 16 13:26:00 2010 From: "Jamin Krinsky jamink|berkeley.edu" To: CCL Subject: CCL:G: TDDFT Message-Id: <-42125-100616130324-2526-Eukia90UMSS9johhVk2CcA-,-server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016364eee108e72bb048928b226 Date: Wed, 16 Jun 2010 10:03:13 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink*_*berkeley.edu] --0016364eee108e72bb048928b226 Content-Type: text/plain; charset=ISO-8859-1 I'm not sure I exactly understand the physical process you are modeling, but if it involves ionization where the ionized product winds up in it's first excited state, then I think you are correct in just adding up the IP and the first excitation energy in the product. If you arrive at the excited state of interest from a higher excited state then the zero oscillator strength is not relevant. Hope this helps. Jamin On Tue, Jun 15, 2010 at 12:08 AM, Liu Jing jliu a cuhk.edu.hk < owner-chemistry_-_ccl.net> wrote: > Dear Jamin, > > What i want to do is to add the first excited energy to the electron > detachment enery and then get the total energy from ground state of > parent ions to the first excited state of product ion.So i'm confused > whehter it is meaningful when oscillator strength =0, can you give me > some hint, thank you. > > Regards > Liu,Jing > > 2010/6/15 Jamin Krinsky jamink++berkeley.edu > > A vanishing oscillator strength does mean that the transition is predicted >> to be unobserved. Whether or not it is technically forbidden depends on the >> molecular symmetry, etc., and I don't know what your system is. In TD-DFT it >> is fairly common to get low-lying, spurious (non-physical) states with >> little or no oscillator strength. Also, if you were calculating triplet >> states from a singlet ground state than all of those will obviously be >> forbidden (but you mentioned that you were studying open-shell systems so >> that's probably not the case). >> Jamin >> >> >> >> On Mon, Jun 14, 2010 at 6:37 PM, Liu Jing jliu]^[cuhk.edu.hk < >> owner-chemistry|a|ccl.net > wrote: >> >>> Dear Jamin, >>> Thank you for your quick reply. >>> Would you like to say sth about the oscillator strengths. In my >>> calculation this value is equal to zero for the first excited state, does >>> it mean this transition is forbidden? >>> >>> Regards >>> Liu, Jing >>> 2010/6/15 Jamin Krinsky jamink()berkeley.edu >>> >>> Dear Jing, >>>> >>>> If you are using Gaussian, you cannot request excited-state >>>> multiplicities different from the ground state for open-shell molecules (the >>>> "singlets" and "triplets" options are ignored). You can of course calculate >>>> the ground-state configuration for each multiplicity and compare energies of >>>> those... Some other programs (Q-Chem included I think) will let you do >>>> spin-flip TDDFT, but you'd want to read up on the subject before attempting >>>> it (I don't know much about it). >>>> >>>> Regards, >>>> Jamin >>>> >>>> >>>> On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk < >>>> owner-chemistry]~[ccl.net > wrote: >>>> >>>>> Dear all, >>>>> >>>>> Can you tell me how to set the spin multiplicity of the excited >>>>> states when a open- >>>>> shell system is concerned? >>>>> >>>>> Thank you and good luck. >>>>> >>>>> Yours Jing >>>>> >>>> >>>> >>>> >>>> -- >>>> Jamin L Krinsky, Ph.D. >>>> Molecular Graphics and Computation Facility >>>> 175 Tan Hall, University of California, Berkeley, CA 94720 >>>> jamink]~[berkeley.edu , 510-643-0616 >>>> http://glab.cchem.berkeley.edu >>>> >>>> >>> >> >> >> -- >> Jamin L Krinsky, Ph.D. >> Molecular Graphics and Computation Facility >> 175 Tan Hall, University of California, Berkeley, CA 94720 >> jamink|a|berkeley.edu , 510-643-0616 >> >> http://glab.cchem.berkeley.edu >> >> > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink_-_berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016364eee108e72bb048928b226 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I'm not sure I exactly understand the physical process you are modeling= , but if it involves ionization where the ionized product winds up in it= 9;s first excited state, then I think you are correct in just adding up the= IP and the first excitation energy in the product. If you arrive at the ex= cited state of interest from a higher excited state then the zero oscillato= r strength is not relevant. Hope this helps.
Jamin


On Tue, Jun 15, 2010 at 12:08 A= M, Liu Jing jliu a cuhk.edu.hk <owner-chemistry_-_ccl= .net> wrote:
Dear=A0Jamin= ,
=A0=A0=A0
=A0 What i want to do is to add the first=A0excited energy to the elec= tron
detachment enery and then=A0get=A0the total energy from ground state o= f
parent ions to the first excited state of product ion.So i'm confu= sed
whehter it is meaningful when oscillator strength =3D0, can you give m= e
some hint, thank you.
=A0
Regards
Liu,Jing

2010/6/15 Jamin Krinsky jamink++berkeley.edu <owner-chemistr= y[a]ccl.net>

A vanishing oscil= lator strength does mean that the transition is predicted to be unobserved.= Whether or not it is technically forbidden depends on the molecular symmet= ry, etc., and I don't know what your system is. In TD-DFT it is fairly = common to get low-lying, spurious (non-physical) states with little or no o= scillator strength. Also, if you were calculating triplet states from a sin= glet ground state than all of those will obviously be forbidden (but you me= ntioned that you were studying open-shell systems so that's probably no= t the case).
Jamin=20



On Mon, Jun 14, 2010 at 6:37 PM, Liu Jing jliu]^= [cuhk.edu.hk <owner-chemistry|a|ccl.net> wrote:
Dear Jamin,
=A0=A0=A0 Thank you for your quick reply.
=A0=A0=A0 Would you like to say sth about the oscillator strengths. In= my
calculation this value is equal to zero for the first excited state, d= oes
it mean this transition is forbidden?
=A0
Regards
Liu, Jing
2010/6/15 Jamin Krinsky jamink()berkeley.edu <<= a href=3D"mailto:owner-chemistry%ccl.net" target=3D"_blank">owner-chemistry= %ccl.net>=20

Dear Jing,
If you are using Gaussian, you cannot request excited-state multiplicities= different from the ground state for open-shell molecules (the "single= ts" and "triplets" options are ignored). You can of course c= alculate the ground-state configuration for each multiplicity and compare e= nergies of those... Some other programs (Q-Chem included I think) will let = you do spin-flip TDDFT, but you'd want to read up on the subject before= attempting it (I don't know much about it).

Regards,
Jamin


On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/.= /cuhk.edu.hk <owner-chemistry]~[ccl.net> wrote:
Dear all,
=A0=A0
=A0=A0Can you tell me how to set the spin multiplicity of the excited = states when a open-
shell system is concerned?
=A0
=A0Thank you and good luck.
=A0
Yours Jing



--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Com= putation Facility
175 Tan Hall, University of California, Berkeley, CA 9= 4720
jamink]~[berke= ley.edu, 510-643-0616
http://glab.cchem.berkeley.edu





--
Jamin L= Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan H= all, University of California, Berkeley, CA 94720
jamink|a|berkeley.edu<= /a>, 510-643-0616=20
=




--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink_-_berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016364eee108e72bb048928b226-- From owner-chemistry@ccl.net Wed Jun 16 15:38:00 2010 From: "Nikolay Novikov nikolay_novikov%%yahoo.com" To: CCL Subject: CCL: Entropy in docking Message-Id: <-42126-100616131144-5951-S/IEftBRuVOIexYVgTFwUQ- -server.ccl.net> X-Original-From: "Nikolay Novikov" Date: Wed, 16 Jun 2010 13:11:43 -0400 Sent to CCL by: "Nikolay Novikov" [nikolay_novikov : yahoo.com] Dear CCL members, Would you advice me on how to account for entropy in protein-ligand docking? What software is used to account for entropy when docking yields several hundreds of docked positions? Thank you all! Sincerely, Nikolay Novikov Ph.D. student,Lviv University, Ukraine From owner-chemistry@ccl.net Wed Jun 16 16:59:01 2010 From: "Andrew Orry andy:_:molsoft.com" To: CCL Subject: CCL: Docking Software for Macrocycles Message-Id: <-42127-100616153835-2329-Xi4btNh2lhk5j8zpYTGeHQ%server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 16 Jun 2010 11:02:45 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy---molsoft.com] John, MolSoft's ICM-Pro http://www.molsoft.com/icm_pro.html software efficiently samples macrocycle ring conformations during the docking process. We offer full-feature trial licenses if you want to test its performance. Thanks, Andy -- Andrew Orry Ph.D. Senior Research Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla CA 92037 Tel: 858-625-2000 x108 Fax: 828-625-2888 On 6/16/2010 7:21 AM, John Furr john.furr/./gmail.com wrote: > Sent to CCL by: "John Furr" [john.furr|gmail.com] > Hey gang, > > I'm looking for advise/tips about docking software that will work well with large macrocycles...19+ ring atoms. Software can be commercial or not. > > Currently we are using the Schrodinger suite of tools with moderate success. However our biggest limitation is that glide does not sample large ring conformations. This means that for every compounds we want to dock we have to first do an upfront conformational analysis and this takes several hours to do in a complete manner. > > To put it in units of time. It takes me about 4 hours per compound to get a docked pose for a single CPU. There are literally times that the chemistry team is faster than me! > > Obviously we are very interested in exploring other options that would allow us to improve our throughput without compromising robustness. > > So gang any advise and or tips? > > Cheers > John Furr> >