If you actually want to include low energy b= ond breaking in you search, have a look at the global reaction mapping from= Ohno & Maeda, forgot the acronym, but I think it was from ca. 2004.

/Per-Ola

Sent from my iPhone

On 7 Dec 2016, at 06:55, Michael Morgan michaelmorgan937%a%gmail.com <o= wner-chemistry*ccl.net> wrote:

Dear All,

I am looking for a program/software to perform a loc= al minimum geometry search. Basically, I will input an optimized minimum ge= ometry of a molecule and a "kick" energy (or temperature), the pr= ogram will use the "kick" energy to overcome energy barriers on PES and find as many as possible other energy minimum g= eometries.

My main research focuses on ab initio calculations, = so I am not familiar with MD programs capable of performing this type of se= arch, although I am sure there must be many. Can someone give me a good sug= gestion?

It would be the best if the program/software could:<= o:p>

1) be simple and easy: I can just input the geometry= and set the "kick" energy/temperature. No script writing.

2) include reliable/popular force field;<= /p>
3) tell me how many times each identified minimum ge= ometry is found during the search;

Free software would be great, but if not we do have = enough fund to purchase.

Any suggestion will be greatly appreciated!

Best regards,

Michael Morgan

Confidentiality Notice: This message is private and may contain confidential and proprieta= ry information. If you have received this message in error, please notify u= s and remove it from your system and note that you must not copy, distribut= e or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message = is not permitted and may be unlawful.

--_000_EE2CB0FD1DD94571A36386B16ED1FC82astrazenecacom_-- From owner-chemistry@ccl.net Wed Dec 7 09:51:00 2016 From: "Gerhard Goldbeck gerhard^^^goldbeck-consulting.com" To: CCL Subject: CCL: software for energy minima search Message-Id: <-52548-161207071736-19311-E89d1liw94YrZPwA/AECLQ%a%server.ccl.net> X-Original-From: Gerhard Goldbeck Content-Type: multipart/alternative; boundary="------------079F9D0DD8E6C43BD474BBE1" Date: Wed, 7 Dec 2016 12:17:25 +0000 MIME-Version: 1.0 Sent to CCL by: Gerhard Goldbeck [gerhard[*]goldbeck-consulting.com] This is a multi-part message in MIME format. --------------079F9D0DD8E6C43BD474BBE1 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Dear Michael, you could also consider a new, powerful and fast data-based approach: https://www.ccdc.cam.ac.uk/solutions/csd-enterprise/applications/conformer-generator/ Most universities have or have access to a licence. Best regards Gerhard * Dr Gerhard Goldbeck * Goldbeck Consulting Ltd * St John's Innovation Centre * Cambridge CB4 0WS * www.materialsmodelling.com * Tel: +44 1223 853201 * Mob: +44 7528 767667 * Skype: Gerhard.Goldbeck * Registered in England No. 7595583 European Materials Modelling Council: http://emmc.info On 07/12/2016 03:51, Michael Morgan michaelmorgan937%a%gmail.com wrote: > > Dear All, > > I am looking for a program/software to perform a local minimum > geometry search. Basically, I will input an optimized minimum geometry > of a molecule and a "kick" energy (or temperature), the program will > use the "kick" energy to overcome energy barriers on PES and find as > many as possible other energy minimum geometries. > > My main research focuses on ab initio calculations, so I am not > familiar with MD programs capable of performing this type of search, > although I am sure there must be many. Can someone give me a good > suggestion? > > It would be the best if the program/software could: > > 1) be simple and easy: I can just input the geometry and set the > "kick" energy/temperature. No script writing. > > 2) include reliable/popular force field; > > 3) tell me how many times each identified minimum geometry is found > during the search; > > Free software would be great, but if not we do have enough fund to > purchase. > > Any suggestion will be greatly appreciated! > > Best regards, > > Michael Morgan > --------------079F9D0DD8E6C43BD474BBE1 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit

Dear Michael,

you could also consider a new, powerful and fast data-based approach:

https://www.ccdc.cam.ac.uk/solutions/csd-enterprise/applications/conformer-generator/

Most universities have or have access to a licence.

Best regards

Gerhard

Dr Gerhard Goldbeck

Goldbeck Consulting Ltd

St John's Innovation Centre

Cambridge CB4 0WS

www.materialsmodelling.com

Tel: +44 1223 853201

Mob: +44 7528 767667

Skype: Gerhard.Goldbeck

Registered in England No. 7595583

European Materials Modelling Council: http://emmc.info

On 07/12/2016 03:51, Michael Morgan michaelmorgan937%a%gmail.com wrote:

Dear All,

�

I am looking for a program/software to perform a local minimum geometry search. Basically, I will input an optimized minimum geometry of a molecule and a "kick" energy (or temperature), the program will use the "kick" energy to overcome energy barriers on PES and find as many as possible other energy minimum geometries.

�

My main research focuses on ab initio calculations, so I am not familiar with MD programs capable of performing this type of search, although I am sure there must be many. Can someone give me a good suggestion?

�

It would be the best if the program/software could:

�

1) be simple and easy: I can just input the geometry and set the "kick" energy/temperature. No script writing.

2) include reliable/popular force field;

3) tell me how many times each identified minimum geometry is found during the search;

�

Free software would be great, but if not we do have enough fund to purchase.

�

Any suggestion will be greatly appreciated!

�

Best regards,

�

Michael Morgan

�

�

--------------079F9D0DD8E6C43BD474BBE1-- From owner-chemistry@ccl.net Wed Dec 7 10:26:00 2016 From: "Franck Chevalier f.chevalier[A]acellera.com" To: CCL Subject: CCL: software for energy minima search Message-Id: <-52549-161207073112-24183-Qi/15h0q537V5ifM5IZkKA,+,server.ccl.net> X-Original-From: "Franck Chevalier" Date: Wed, 7 Dec 2016 07:31:10 -0500 Sent to CCL by: "Franck Chevalier" [f.chevalier*o*acellera.com] Hi Michael, You can use HTMD (free for non-profit uses) to parameterize your molecule (a ligand, I assume) and then use adaptive sampling MD on the soft/rotatable torsions to explore the PES efficiently. Parameterization: install, and run `parameterize -h` Adaptive: https://www.htmd.org/docs/latest/tutorials/adaptive-sampling- basics.html General documentation: https://www.htmd.org/docs/latest/index.html Any questions, you can use: https://github.com/Acellera/htmd/issues or send us an e-mail to support%acellera.com The Acellera team. > "Michael Morgan michaelmorgan937%a%gmail.com" wrote: > > Sent to CCL by: "Michael Morgan" [michaelmorgan937:_:gmail.com] > This is a multipart message in MIME format. > > ------=_NextPart_000_0031_01D2500A.F256DE40 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > Dear All, > > > > I am looking for a program/software to perform a local minimum geometry > search. Basically, I will input an optimized minimum geometry of a molecule > and a "kick" energy (or temperature), the program will use the "kick" energy > to overcome energy barriers on PES and find as many as possible other energy > minimum geometries. > > > > My main research focuses on ab initio calculations, so I am not familiar > with MD programs capable of performing this type of search, although I am > sure there must be many. Can someone give me a good suggestion? > > > > It would be the best if the program/software could: > > > > 1) be simple and easy: I can just input the geometry and set the "kick" > energy/temperature. No script writing. > > 2) include reliable/popular force field; > > 3) tell me how many times each identified minimum geometry is found during > the search; > > > > Free software would be great, but if not we do have enough fund to purchase. > > > > > Any suggestion will be greatly appreciated! > > > > Best regards, > > > > Michael Morgan > > > > > > > ------=_NextPart_000_0031_01D2500A.F256DE40 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> http-equiv=3DContent-Type content=3D"text/html; = > charset=3Dus-ascii"> (filtered medium)"> link=3D"#0563C1" vlink=3D"#954F72">

class=3DMsoNormal>Dear All,

class=3DMsoNormal>

I am looking = > for a program/software to perform a local minimum geometry search. = > Basically, I will input an optimized minimum geometry of a molecule and = > a "kick" energy (or temperature), the program will use the = > "kick" energy to overcome energy barriers on PES and find as = > many as possible other energy minimum geometries.

class=3DMsoNormal>

My main = > research focuses on ab initio calculations, so I am not familiar with MD = > programs capable of performing this type of search, although I am sure = > there must be many. Can someone give me a good suggestion? = >

class=3DMsoNormal>It would be the best if the program/software = > could:

class=3DMsoNormal>1) be simple and easy: I can just input the geometry = > and set the "kick" energy/temperature. No script = > writing.

2) include reliable/popular = > force field;

3) tell me how many = > times each identified minimum geometry is found during the = > search;

class=3DMsoNormal>Free software would be great, but if not we do have = > enough fund to purchase.

class=3DMsoNormal>

Any = > suggestion will be greatly appreciated!

class=3DMsoNormal>

Best = > regards,

class=3DMsoNormal>Michael Morgan

class=3DMsoNormal>

> ------=_NextPart_000_0031_01D2500A.F256DE40-- > > From owner-chemistry@ccl.net Wed Dec 7 11:01:00 2016 From: "Alcides Simao alsimao() gmail.com" To: CCL Subject: CCL: software for energy minima search Message-Id: <-52550-161207075134-1885-A6L6BVUmH5IptbV287yqZg**server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=089e013c6b2ab24c45054310fabf Date: Wed, 07 Dec 2016 12:51:17 +0000 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao###gmail.com] --089e013c6b2ab24c45054310fabf Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Michael, Per-Ola was talking about the Scaled Hypersphere Search (SHS) method by Ohno and Maeda (Ohno, K.; Maeda, S. *Chem. Phys. Lett.* *2004*, *384*, 277) Best, Alcides Norrby, Per-Ola Per-Ola.Norrby=3D=3D=3Dastrazeneca.com escreveu no dia quarta, 7/12/2016 =C3=A0s 12:38: > Dear Michael, > > These tools have been more developed for molecular mechanics, but the > principles are the same for QM. What you describe is basically the method > by Saunders. It's not the best method; a random cartesian displacement ca= n > generate strange, strained structures that take a long time to minimize. = It > is more productive if you put some intelligence into the kick, basically > avoiding stretching bonds too much. The best one I know for local searche= s > of geometry is the Low Mode search, requires 2nd derivatives (Hessian). F= or > more global search, I recommend a torsional kick. A very efficient > combination of these, for global searching in MM, is available in > MacroModel, www.schrodinger.com . In that package, you can search using > MM, then refine using QM of your choice in Jaguar. > > If you actually want to include low energy bond breaking in you search, > have a look at the global reaction mapping from Ohno & Maeda, forgot the > acronym, but I think it was from ca. 2004. > > /Per-Ola > > Sent from my iPhone > > On 7 Dec 2016, at 06:55, Michael Morgan michaelmorgan937%a%gmail.com < > owner-chemistry,,ccl.net> wrote: > > Dear All, > > > > I am looking for a program/software to perform a local minimum geometry > search. Basically, I will input an optimized minimum geometry of a molecu= le > and a "kick" energy (or temperature), the program will use the "kick" > energy to overcome energy barriers on PES and find as many as possible > other energy minimum geometries. > > > > My main research focuses on ab initio calculations, so I am not familiar > with MD programs capable of performing this type of search, although I am > sure there must be many. Can someone give me a good suggestion? > > > > It would be the best if the program/software could: > > > > 1) be simple and easy: I can just input the geometry and set the "kick" > energy/temperature. No script writing. > > 2) include reliable/popular force field; > > 3) tell me how many times each identified minimum geometry is found durin= g > the search; > > > > Free software would be great, but if not we do have enough fund to > purchase. > > > > Any suggestion will be greatly appreciated! > > > > Best regards, > > > > Michael Morgan > > > > > > ------------------------------ > > *Confidentiality Notice: *This message is private and may contain > confidential and proprietary information. If you have received this messa= ge > in error, please notify us and remove it from your system and note that y= ou > must not copy, distribute or take any action in reliance on it. Any > unauthorized use or disclosure of the contents of this message is not > permitted and may be unlawful. > > -- Alcides Pinto Sim=C3=A3o, AMRSC, PhD. Student University of Coimbra Office: +351 239 852 080 / Fax: +351 239 827 703 Departamento de Qu=C3=ADmica da Universidade de Coimbra, 3004-535 COIMBRA, PORTUGAL Website: http://www.qui.uc.pt/ This e-mail message may contain confidential or legally privileged information and is intended only for the use of the intended recipient(s). Any unauthorized disclosure, dissemination, distribution, copying or the taking of any action in reliance on the information herein is prohibited. E-mails are not secure and cannot be guaranteed to be error free as they can be intercepted, amended, or contain viruses. Anyone who communicates with us by e-mail is deemed to have accepted these risks. University of Coimbra is not responsible for errors or omissions in this message and denies any responsibility for any damage arising from the use of e-mail. Any opinion and other statement contained in this message and any attachment are solely those of the author and do not necessarily represent those of the company. [image: Follow me on ResearchGate] --089e013c6b2ab24c45054310fabf Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Michael,

Per-Ola was talking about= the Scaled Hypersphere Search (SHS) method by= Ohno and Maeda (Ohno, K.; Maeda, S.=C2=A0Chem. Phys. Lett.=C2=A02004,=C2=A038= 4, 277)

Best,=

Alcides

Norrby, Per-Ola Per-Ola.Norrby=3D=3D=3Dastrazeneca.com <owner-chemistry##ccl.net> escreveu no dia quarta, 7/12/2016 = =C3=A0s 12:38:

Dear Michael,

The= se tools have been more developed for molecular mechanics, but the principl= es are the same for QM. What you describe is basically the method by Saunde= rs. It's not the best method; a random cartesian displacement can gener= ate strange, strained structures that take a long time to minimize. It is more= productive if you put some intelligence into the kick, basically avoiding = stretching bonds too much. The best one I know for local searches of geomet= ry is the Low Mode search, requires 2nd derivatives (Hessian). For more global search, I recommend a torsional= kick. A very efficient combination of these, for global searching in MM, i= s available in MacroModel, www.schrodinger.com . In that package, you can search using MM, then = refine using QM of your choice in Jaguar.

If = you actually want to include low energy bond breaking in you search, have a= look at the global reaction mapping from Ohno & Maeda, forgot the acro= nym, but I think it was from ca. 2004.

/Pe= r-Ola

Sent from my iPhone

On 7 Dec 2016, at 06:55, Michael Morgan michaelmorgan937%a%gmail.com <owner-chemistry,,ccl.net> wrote:

Dear All,

=C2=A0

I am looking for a program/software to per= form a local minimum geometry search. Basically, I will input an optimized = minimum geometry of a molecule and a "kick" energy (or temperatur= e), the program will use the "kick" energy to overcome energy barriers on PES and find as many as possible other energy minimum g= eometries.

=C2=A0

My main research focuses on ab initio calc= ulations, so I am not familiar with MD programs capable of performing this = type of search, although I am sure there must be many. Can someone give me = a good suggestion?

=C2=A0

It would be the best if the program/softwa= re could:

=C2=A0

1) be simple and easy: I can just input th= e geometry and set the "kick" energy/temperature. No script writi= ng.

2) include reliable/popular force field;

3) tell me how many times each identified = minimum geometry is found during the search;

=C2=A0

Free software would be great, but if not w= e do have enough fund to purchase.

=C2=A0

Any suggestion will be greatly appreciated= !

=C2=A0

Best regards,

=C2=A0

Michael Morgan<= u class=3D"gmail_msg">

=C2=A0

=C2=A0

Confidentiality Notice: This message is private and may contain confidential and proprieta= ry information. If you have received this message in error, please notify u= s and remove it from your system and note that you must not copy, distribut= e or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message = is not permitted and may be unlawful.

Alcides Pinto Sim=C3=A3o, AMRSC, PhD. Studen= t

= University of Coimbra=C2=A0Office:=C2=A0<= span id=3D"inbox-inbox-office-input" class=3D"inbox-inbox-txt" style=3D"col= or:rgb(153,153,153)">+351 239 852 080=C2=A0/ Fax:= =C2=A0+351 239 827 703=C2=A0
Departamento de Qu= =C3=ADmica da Universidade de Coimbra, 3004-535 COIMBRA, PORTUGALWebsite:=C2=A0http://www= .qui.uc.pt/

This e-mail message may contain confidential or legally privileged= information and is intended only for the use of the intended recipient(s).= Any unauthorized disclosure, dissemination, distribution, copying or the t= aking of any action in reliance on the information herein is prohibited. E-= mails are not secure and cannot be guaranteed to be error free as they can = be intercepted, amended, or contain viruses. Anyone who communicates with u= s by e-mail is deemed to have accepted these risks. University of Coimbra i= s not responsible for errors or omissions in this message and denies any re= sponsibility for any damage arising from the use of e-mail. Any opinion and= other statement contained in this message and any attachment are solely th= ose of the author and do not necessarily represent those of the company.

--089e013c6b2ab24c45054310fabf--