From owner-chemistry@ccl.net Fri Nov 28 00:55:00 2008 From: "Berkholz, Donnie - dberkholz:-:gentoo.org" To: CCL Subject: CCL: Conformational searches with right Ramachandran angles Message-Id: <-38193-081127163608-31867-XQgbHFkI4CAcusvWbDmiOg_+_server.ccl.net> X-Original-From: "Berkholz, Donnie -" Content-Disposition: inline Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="5vNYLRcllDrimb99" Date: Thu, 27 Nov 2008 12:38:11 -0800 MIME-Version: 1.0 Sent to CCL by: "Berkholz, Donnie -" [dberkholz*|*gentoo.org] --5vNYLRcllDrimb99 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On 17:10 Thu 27 Nov , Jean-Christophe Poully poully.%a%.galilee.univ-pari= s13.fr wrote: > I would like to know if there is one software that can perform accurate= =20 > conformational searches on peptides containing at least 5 amino acids and= =20 > that have the ability to speed up the calculation by scanning only=20 > Ramachandran angles compatible with typical structures like alpha-helix= =20 > and beta-sheet... Most of the conformational search softwares do a=20 > Monte-Carlo or systematic search, but the majority of the structures=20 > found have not allowed Ramachandran angles. Thank you very much by=20 > advance! Anything that uses an empirically derived peptide fragment library=20 should work. Rosetta is one example. I think Modeller takes the same=20 approach, and I suspect you might find it a bit easier to use. --=20 Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com --5vNYLRcllDrimb99 Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.9 (GNU/Linux) iEYEABECAAYFAkkvBTMACgkQXVaO67S1rtvjgwCdGgY/2CsZp9NplnBdTnVGrJyg zfEAoPFylHwrMi8pgO9c+YMNMs6nmJko =qKQj -----END PGP SIGNATURE----- --5vNYLRcllDrimb99-- From owner-chemistry@ccl.net Fri Nov 28 10:43:00 2008 From: "Agesilaos George Hantzis ahatz(a)chemistry.upatras.gr" To: CCL Subject: CCL:G: About the "SCF is confused error" in G03W Message-Id: <-38194-081128104119-10930-DX3AaX60eHsf+zB3Ps0h8A##server.ccl.net> X-Original-From: "Agesilaos George Hantzis" Date: Fri, 28 Nov 2008 10:41:15 -0500 Sent to CCL by: "Agesilaos George Hantzis" [ahatz(a)chemistry.upatras.gr] I am aware that some users used to have the following message while trying to converge the SCF using G03W defaults:Density matrix is not changing but DIIS error= (A NUMBER) The SCF is confused. I had this problem too using G03W to optimize a structure. However i have found that if you use Pula's DIIS (the default in earlier versions of Gaussian) without Fermi broadening and damping etc my case converged without showing the aforementioned error message. I think the IOp for the use of Pulay's DIIS (without EDIIS and CDIIS) is IOp(5/22=2). Hope that helps a bit! From owner-chemistry@ccl.net Fri Nov 28 11:20:00 2008 From: "Aneta Manningtonova amanningtonova*|*inforsense.com" To: CCL Subject: CCL: Conformational searches with right Ramachandran angles Message-Id: <-38195-081127132821-21754-ojeTGSJ58dQiffzb3z0E2Q||server.ccl.net> X-Original-From: "Aneta Manningtonova" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C950B9.5BC30A99" Date: Thu, 27 Nov 2008 12:55:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Aneta Manningtonova" [amanningtonova^inforsense.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C950B9.5BC30A99 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mr Poully, =20 Thank you for your request. My colleague Andreas Ritter will get in = touch with you shortly in regards to this matter. =20 Kindest regards =20 Aneta Manningtonova | Office Administrator | InforSense=20 Colet Court | 100 Hammersmith Road | London W6 7JP |=20 United Kingdom amanningtonova%%inforsense.com | +44 (0)20 8237 8440| www.inforsense.com =20 =20 InforSense 5.0: The Next Generation BI Platform InforSense Disclaimer This email is confidential and intended solely for the use of the = individual to whom it is addressed, and not intended to be further = distributed without explicit prior approval of the sender. Any views or = opinions presented are solely those of the author and do not necessarily = represent those of InforSense Limited unless explicitly indicated. If = you are not the intended recipient, be advised that you have received = this email in error and that any use, dissemination, forwarding, = printing, or copying of this email is strictly prohibited. =20 =20 ________________________________ > From: owner-chemistry+jbandy=3D=3Dinforsense.com%%ccl.net = [mailto:owner-chemistry+jbandy=3D=3Dinforsense.com%%ccl.net] On Behalf Of = Jean-Christophe Poully poully.%%.galilee.univ-paris13.fr Sent: 27 November 2008 16:10 To: Aneta Manningtonova Subject: CCL: Conformational searches with right Ramachandran angles =20 Dear all, I would like to know if there is one software that can perform accurate = conformational searches on peptides containing at least 5 amino acids = and that have the ability to speed up the calculation by scanning only = Ramachandran angles compatible with typical structures like alpha-helix = and beta-sheet... Most of the conformational search softwares do a = Monte-Carlo or systematic search, but the majority of the structures = found have not allowed Ramachandran angles. Thank you very much by = advance! Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853 ------_=_NextPart_001_01C950B9.5BC30A99 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Mr = Poully,

 

Thank you for your request. My = colleague Andreas Ritter will get in touch with you shortly in regards to this = matter.

 

Kindest = regards

 

Aneta Manningtonova | Office Administrator | InforSense

Colet = Court | 100 Hammersmith Road | London W6 7JP |

United = Kingdom
amanningtonova%%inforsense.com | +44 (0)20 8237 = 8440| www.inforsense.com=

 

=

 <= /span>

= InforSense 5.0: The Next Generation BI Platform

InforSense = Disclaimer
This email is confidential and intended solely for the use of the = individual to whom it is addressed, and not intended to be further distributed without explicit prior approval of the sender. Any views or opinions presented = are solely those of the author and do not necessarily represent those of = InforSense Limited unless explicitly indicated. If you are not the intended = recipient, be advised that you have received this email in error and that any use, = dissemination, forwarding, printing, or copying of this email is strictly = prohibited.

 <= /span>

 

=

From: owner-chemistry+jbandy=3D=3Dinforsense.com%%ccl.net [mailto:owner-chemistry+jbandy=3D=3Dinforsense.com%%ccl.net] On Behalf Of Jean-Christophe = Poully poully.%%.galilee.univ-paris13.fr
Sent: 27 November 2008 = 16:10
To: Aneta = Manningtonova
Subject: CCL: = Conformational searches with right Ramachandran angles

 


Dear all,

I would like to know if there is one software that can perform accurate = conformational searches on peptides containing at least 5 amino acids and that have the ability to speed up the calculation by scanning only Ramachandran angles compatible with typical = structures like alpha-helix and beta-sheet... Most of the conformational search = softwares do a Monte-Carlo or systematic search, but the majority of the = structures found have not allowed Ramachandran angles. Thank you very much by = advance!




Jean-Christophe Poully

Doctorant dans l'=E9quipe AMIBES
Laboratoire de Physique des Lasers
Institut Galil=E9e
99, avenue JB Cl=E9ment
93430 VILLETANEUSE

Bureau B002
0149403853

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