From owner-chemistry@ccl.net Sat May 29 05:00:00 2010 From: "jeffle07 jeffle07[]163.com" To: CCL Subject: CCL: how to build the protein loop Message-Id: <-42014-100527091334-5850-xWYC+K4Jj3yW7JW3WRfmHQ{:}server.ccl.net> X-Original-From: jeffle07 Content-Type: multipart/alternative; boundary="----=_Part_100633_25636086.1274965995427" Date: Thu, 27 May 2010 21:13:15 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: jeffle07 [jeffle07=163.com] ------=_Part_100633_25636086.1274965995427 Content-Type: text/plain; charset=gbk Content-Transfer-Encoding: base64 RGVhciBhbGwsCiAgICAgICAgV2UgYXJlIGdvaW5nIHRvIGJ1aWxkIGEgcHJvdGVpbiBtb2RlbCBm b3IgTUQgc2ltdWxhdGlvbi4gQnV0IHNldmVyYWwgbG9vcCByZWdpb25zIChhYm91dCA1MCByZXNp ZHVlcyBpbiBlYWNoIG1pc3NlZCBsb29wKSBhcmUgbWlzc2VkIGluIHRoZSBjcnlzdGFsIHN0cnVj dHVyZS4gQ291bGQgc29tZW9uZSBrbm93IGhvdyB0byBidWlsZCB0aGVzZSByZWdpb25zIHByb3Bl cmx5PyBJcyB0aGVyZSBhbnkgcGFja2FnZSBvciB3ZWJzZXJ2ZXIgdGhhdCBjYW4gZG8gdGhlIGpv Yj8KIApNYW55IHRoYW5rcy4KIApKZWZmLiBZYW5nICA= ------=_Part_100633_25636086.1274965995427 Content-Type: text/html; charset=gbk Content-Transfer-Encoding: base64 PERJVj5EZWFyIGFsbCw8L0RJVj4KPERJVj4mbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsm bmJzcDsmbmJzcDsmbmJzcDtXZSBhcmUgZ29pbmcgdG8gYnVpbGQgYSBwcm90ZWluIG1vZGVsIGZv ciBNRCBzaW11bGF0aW9uLiBCdXQmbmJzcDtzZXZlcmFsIGxvb3AgcmVnaW9ucyAoYWJvdXQgNTAg cmVzaWR1ZXMgaW4gZWFjaCBtaXNzZWQgbG9vcCkgYXJlIG1pc3NlZCBpbiB0aGUgY3J5c3RhbCBz dHJ1Y3R1cmUuJm5ic3A7Q291bGQgc29tZW9uZSBrbm93IGhvdyB0byBidWlsZCB0aGVzZSByZWdp b25zIHByb3Blcmx5PyBJcyB0aGVyZSBhbnkmbmJzcDtwYWNrYWdlIG9yIHdlYnNlcnZlciB0aGF0 IGNhbiBkbyB0aGUmbmJzcDtqb2I/PC9ESVY+CjxESVY+Jm5ic3A7PC9ESVY+CjxESVY+TWFueSB0 aGFua3MuPC9ESVY+CjxESVY+Jm5ic3A7PC9ESVY+CjxESVY+SmVmZi4gWWFuZyZuYnNwOyZuYnNw OzwvRElWPjxicj48YnI+PHNwYW4gdGl0bGU9Im5ldGVhc2Vmb290ZXIiLz48aHIvPgo8YSBocmVm PSJodHRwOi8veW0uMTYzLmNvbS8/ZnJvbT1vZDMiIHRhcmdldD0iX2JsYW5rIj7N+NLXzqrW0NCh xvPStcPit9HM4bmpxvPStdPKz+SjqNfU1vfT8sP7o6k8L2E+Cjwvc3Bhbj4= ------=_Part_100633_25636086.1274965995427-- From owner-chemistry@ccl.net Sat May 29 07:25:01 2010 From: "Arun Venkatnathan arunv1973 . yahoo.com" To: CCL Subject: CCL: Cage compounds Message-Id: <-42015-100529072311-12747-cjurB8JNzss1Ykx9cqOyPg]|[server.ccl.net> X-Original-From: Arun Venkatnathan Content-Type: multipart/alternative; boundary="0-1905974549-1275132186=:28359" Date: Sat, 29 May 2010 04:23:06 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Arun Venkatnathan [arunv1973#%#yahoo.com] --0-1905974549-1275132186=:28359 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,=20 Can anyone recommend any free software available to generate different conf= igurations (coordinates) for cage compounds (e.g. gas hydrates).=20 Thanks, Arun=20 Dr. Arun Venkatnathan Assistant Professor, Chemistry Indian Institute of Science Education and Research, Pune Pune 411021 India =A0 =0A=0A=0A --0-1905974549-1275132186=:28359 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,

Ca= n anyone recommend any free software available to generate different config= urations (coordinates) for cage compounds (e.g. gas hydrates).

Than= ks,
Arun

Dr. Arun Venkatnathan
Assistant Professor, Chemistry=
Indian Institute of Science Education and Research, Pune
Pune 411021= India
 

=0A=0A --0-1905974549-1275132186=:28359-- From owner-chemistry@ccl.net Sat May 29 08:56:00 2010 From: "pascal boulet pascal.boulet*|*univ-provence.fr" To: CCL Subject: CCL: how to build the protein loop Message-Id: <-42016-100529084517-6818-5QLesAwJ6EbfDqGYACnAqA[*]server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=x-gbk Date: Sat, 29 May 2010 14:45:00 +0200 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet..univ-provence.fr] -----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello,

Tinker has a utility program to build proteins and DNA. This might be
helpful.

Hope this help,
Pascal



Le 27/05/2010 15:13, jeffle07 jeffle07[]163.com a écrit :
> Dear all, We are going to build a protein model for MD simulation.
> But several loop regions (about 50 residues in each missed loop)
> are missed in the crystal structure. Could someone know how to
> build these regions properly? Is there any package or webserver
> that can do the job?
>
> Many thanks.
>
> Jeff. Yang
>
>
> ----------------------------------------------------------------------
>
>
网易为中小企业免费提供企业邮箱（自主域名）
> <http://ym.163.com/?from=od3>

- --
Dr. pascal Boulet, computational chemist
University of Aix-Marseille I
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)491.63.71.17
Fax. (+33) (0)491.63.71.11
**********
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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iEYEARECAAYFAkwBDEsACgkQNLjdBN1V75neLgCeKTi+eWS7mMSFBaGAwVFY8SkR
T5YAnix8HncxzGl1tZY0WrroIVDhpO9v
=AvQN
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From owner-chemistry@ccl.net Sat May 29 09:31:00 2010 From: "Emran Heshmati heshmaty^^^yahoo.com" To: CCL Subject: CCL:G: in solvent Message-Id: <-42017-100529083912-19682-SlKByiMc6leJoLdjapfFEQ]=[server.ccl.net> X-Original-From: Emran Heshmati Content-Type: multipart/alternative; boundary="0-2059142009-1275136686=:68677" Date: Sat, 29 May 2010 05:38:06 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Emran Heshmati [heshmaty : yahoo.com] --0-2059142009-1275136686=:68677 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear all =A0 I want to optimize a modified dipeptide structure (CH3-lysine-serinephospha= te-NH2)=A0in solvent water using G 03. "# b3lyp/6-31+g* fopt=3D(maxcycle=3D= 10000) SCRF=3D(DIPOLE,a0=3D5.40,solvent=3Dwater) scf=3Dtight"=20 This structure has a positive charge in lysine and a negative charge in pho= sphate. but it has error termination as blow:=20 "Error termination via Lnk1e in /home/computation/g03/l502.exe" and seeing = in GAUSSVIEW, the output structure was fragmented. Can anyone help me?=20 =A0 Best Regards Emran Heshmati P Save a tree... please don't print this e-mail unless you really need to= =0A=0A --0-2059142009-1275136686=:68677 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all  
I want to = optimize a modified dipeptide structure (CH3-lysine-serinephosphate-NH2)&nb= sp;in solvent water using G 03. "# b3lyp/6-31+g* fopt=3D(maxcycle=3D10000) = SCRF=3D(DIPOLE,a0=3D5.40,solvent=3Dwater) scf=3Dtight" =
This struc= ture has a positive charge in lysine and a negative charge in phosphate. bu= t it has error termination as blow:
"Error ter= mination via Lnk1e in /home/computation/g03/l502.exe" and seeing in GAUSSVI= EW, the output structure was fragmented. Can anyone help me? =

&nb= sp;
Best Regards
Emran = Heshmati
P Save a tree... please don't print this e-mail unless y= ou really need to

--0-2059142009-1275136686=:68677-- From owner-chemistry@ccl.net Sat May 29 10:06:00 2010 From: "Agrafiotis, Dimitris K. PRDUS DAGRAFIO#its.jnj.com" To: CCL Subject: CCL: how to build the protein loop Message-Id: <-42018-100529092113-11364-jfV6tO3fFToEnzxvQTowRw . server.ccl.net> X-Original-From: "Agrafiotis, Dimitris K. [PRDUS]" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CAFF31.C8D3496E" Date: Sat, 29 May 2010 09:21:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Agrafiotis, Dimitris K. [PRDUS]" [DAGRAFIO a its.jnj.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01CAFF31.C8D3496E Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Jeff, =20 We have developed a very efficient method for building protein loops, = described in the following article: =20 http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1= 000478 =20 Please contact me directly if you are interested in using it. Thanks. =20 ____________________________________________________=20 Dimitris Agrafiotis, Johnson & Johnson PRD, Welsh & McKean Roads, Spring = House, PA 19477, (215) 628-6814, dagrafio/a\its.jnj.com, = http://www.dimitris-agrafiotis.com=20 =20 > From: owner-chemistry+dagrafio=3D=3Dprdus.jnj.com/a\ccl.net = [mailto:owner-chemistry+dagrafio=3D=3Dprdus.jnj.com/a\ccl.net] On Behalf = Of pascal boulet pascal.boulet*|*univ-provence.fr Sent: Saturday, May 29, 2010 8:45 AM To: Agrafiotis, Dimitris K. [PRDUS] Subject: CCL: how to build the protein loop =20 Sent to CCL by: pascal boulet [pascal.boulet..univ-provence.fr]=20 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello, Tinker has a utility program to build proteins and DNA. This might be helpful. Hope this help, Pascal Le 27/05/2010 15:13, jeffle07 jeffle07[]163.com a =A8=A6crit : > Dear all, We are going to build a protein model for MD simulation.=20 > But several loop regions (about 50 residues in each missed loop) > are missed in the crystal structure. Could someone know how to > build these regions properly? Is there any package or webserver > that can do the job? >=20 > Many thanks. >=20 > Jeff. Yang >=20 >=20 >=20 ---------------------------------------------------------------------- > >=20 =CD=F8=D2=D7=CE=AA=D6=D0=D0=A1=C6=F3=D2=B5=C3=E2=B7=D1=CC=E1=B9=A9=C6=F3=D2= =B5=D3=CA=CF=E4=A3=A8=D7=D4=D6=F7=D3=F2=C3=FB=A3=A9 > =20 - --=20 Dr. pascal Boulet, computational chemist University of Aix-Marseille I Laboratoire Chimie Provence, UMR 6264 Group of Theoretical Chemistry Avenue Normandie-Niemen 13397 Marseille Cedex 20 France ********** Tel. (+33) (0)491.63.71.17 Fax. (+33) (0)491.63.71.11 ********** http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkwBDEsACgkQNLjdBN1V75neLgCeKTi+eWS7mMSFBaGAwVFY8SkR T5YAnix8HncxzGl1tZY0WrroIVDhpO9v =3DAvQN -----END PGP SIGNATURE----- -=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 the strange characters on the top line to the /a\ sign. You can = alsoE-mail to = subscribers: CHEMISTRY/a\ccl.net or use: =E-mail to = administrators: CHEMISTRY-REQUEST/a\ccl.net or use ==Before posting, check wait = time at: http://www.ccl.netConferences: = http://server.ccl.net/chemistry/announcements/conferences/ Search = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your = mail bounces from CCL with 5.7.1 error, check: =RTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/=20 ------_=_NextPart_001_01CAFF31.C8D3496E Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Jeff,

 

We have developed a very efficient method for building protein loops, described in the following article:

 

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%= 2Fjournal.pcbi.1000478

 

Please contact me directly if you are interested in = using it. Thanks.

 

____________________________________________________
Dimitris Agrafiotis, Johnson & Johnson PRD, = Welsh = & McKean Roads, Spring House, PA 19477, (215) 628-6814, dagrafio/a\its.jnj.com, http://www.dimitris-agrafiotis.com

 

From: owner-chemistry+dagrafio=3D=3Dprdus.jnj.com/a\ccl.net [mailto:owner-chemistry+dagrafio=3D=3Dprdus.jnj.com/a\ccl.net] On = Behalf Of pascal boulet pascal.boulet*|*univ-provence.fr
Sent: Saturday, May 29, 2010 8:45 AM
To: Agrafiotis, Dimitris K. [PRDUS]
Subject: CCL: how to build the protein loop

 

Sent to CCL by: pascal boulet [pascal.boulet..univ-provence.fr]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello,

Tinker has a utility program to build proteins and DNA. This might = be
helpful.

Hope this help,
Pascal



Le 27/05/2010 15:13, jeffle07 jeffle07[]163.com a =A8=A6crit :
> Dear all, We are going to build

a protein model for MD simulation.

> But several loop regions (about 50 residues in = each missed loop)

> are missed in the crystal structure. Could = someone know how to

> build these regions properly? Is there any = package or webserver

> that can do the job?

>

> Many thanks.

>

> Jeff. Yang

>

>

> 

-------------------------------------------------------= ---------------

>

>
=CD=F8=D2=D7=CE=AA=D6=D0=D0=A1=C6=F3=D2=B5=C3=E2=B7=D1=CC=E1=B9=A9=C6=F3=D2= =B5=D3=CA=CF=E4=A3=A8=D7=D4=D6=F7=D3=F2=C3=FB=A3=A9
>

<http://ym.163.com/?from=3Dod3&= gt;

- --
Dr. pascal Boulet, computational chemist
University of Aix-Marseille I
Laboratoire Chimie Provence, UMR 6264
Group of Theoretical Chemistry
Avenue Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)491.63.71.17
Fax. (+33) (0)491.63.71.11
**********
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/b= oulet
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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iEYEARECAAYFAkwBDEsACgkQNLjdBN1V75neLgCeKTi+eWS7mMSFBaGAwVFY8SkR
T5YAnix8HncxzGl1tZY0WrroIVDhpO9v
=3DAvQN
-----END PGP SIGNATURE-----

-=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 the strange characters on the = top line to the /a\ sign. You can also look up the X-Original-From: line in the = mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to = administrators: CHEMISTRY-REQUEST/a\ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait = time at: http://www.ccl.netSearch = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail bounces = > from CCL with 5.7.1 error, check:=

------_=_NextPart_001_01CAFF31.C8D3496E-- From owner-chemistry@ccl.net Sat May 29 12:11:01 2010 From: "S Bear soaringbear*yahoo.com" To: CCL Subject: CCL: how to build the protein loop Message-Id: <-42019-100529120837-13882-uYiJq6mEfAsf4SDpCfpCXw:server.ccl.net> X-Original-From: "S Bear" Date: Sat, 29 May 2010 12:08:35 -0400 Sent to CCL by: "S Bear" [soaringbear+/-yahoo.com] Loop building is an art mainly for just a few residues. Recall the reason that segment lacks a crystal structure is likely due to floppiness. 50 residues is way too long and floppy to get more than a wild guess. Soaring Bear From owner-chemistry@ccl.net Sat May 29 12:46:00 2010 From: "Emmanuel Aubert emmanuel.aubert!A!crm2.uhp-nancy.fr" To: CCL Subject: CCL:G: Laplacian of the total electron density in G09(03) Message-Id: <-42020-100529113226-28335-d2Khti3aqzE/eCF3HaaaoA*server.ccl.net> X-Original-From: "Emmanuel Aubert" Date: Sat, 29 May 2010 11:32:25 -0400 Sent to CCL by: "Emmanuel Aubert" [emmanuel.aubert__crm2.uhp-nancy.fr] Dear all, does anyone knows how to get the Laplacian of the total electron density with Gaussian09 (or 03) program ? (I tried to create a cub from the .fchk file, with the Laplacian keyword : then there are five record in the cub file, the first is the density, the next three are the gradient (I not sure of that) and the last the Laplacian, but it seems to me that's only the Laplacian of the valence density). Best regards, Emmanuel. From owner-chemistry@ccl.net Sat May 29 13:21:00 2010 From: "Radoslaw Kaminski rkaminski.rk-#-gmail.com" To: CCL Subject: CCL: Crystal Structure vs optimized structure Message-Id: <-42021-100528085320-5217-A66yDsMjOIy3+3674TvTkA()server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0015174c0f143270ab0487a6fd9c Date: Fri, 28 May 2010 08:53:09 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk|gmail.com] --0015174c0f143270ab0487a6fd9c Content-Type: text/plain; charset=ISO-8859-1 Hi William, I don't really get the point why are you worried. Of course you can do it. However, you have to remember that such approach will lead to neglecting of intermolacular interactions, and crystal field in general. If you look in archive I was commenting on this some time ago (a year or so). The think I could suggest to do is to take the best possible coordinates from the crystal (preferably from high-resolution measurement), keep the heavy atoms constant and optimize hydrogen atom positions. Also, if you look at the literature these could lead to different interaction energies (because the system is relaxed or not etc.). Always take care while analysing the results! Short question: what does it mean "high level" for you? Hope this helps somehow. Cheers, Radek 2010/5/28 William Flak williamflak---yahoo.com > > Sent to CCL by: "William Flak" [williamflak]^[yahoo.com] > Dear CCL > I was wondering if I can calculate an interaction properties between two > molecules based on crystal structure without optimization? Optimization > with > high level couldn't give me the crystal structure. > Any comment would be appreciated. > W. Flak> > > --0015174c0f143270ab0487a6fd9c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi William,

I don't really get the point why are you worried. Of= course you can do it. However, you have to remember that such approach wil= l lead to neglecting of intermolacular interactions, and crystal field in g= eneral. If you look in archive I was commenting on this some time ago (a ye= ar or so). The think I could suggest to do is to take the best possible coo= rdinates from the crystal (preferably from high-resolution measurement), ke= ep the heavy atoms constant and optimize hydrogen atom positions. Also, if = you look at the literature these could lead to different interaction energi= es (because the system is relaxed or not etc.). Always take care while anal= ysing the results!

Short question: what does it mean "high level" for you?
Hope this helps somehow.

Cheers,

Radek


2010/5/28 William Flak williamflak---yahoo.com <owner-chemistry!=!ccl.net>

Sent to CCL by: "William =A0Flak" [williamflak]^[yahoo.com]
Dear CCL
I was wondering if I can calculate an interaction properties between two molecules based on crystal structure without optimization? Optimization wit= h
high level couldn't give me the crystal structure.
Any comment would be appreciated.
W. Flak



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--0015174c0f143270ab0487a6fd9c-- From owner-chemistry@ccl.net Sat May 29 15:07:00 2010 From: "William Flak williamflak__yahoo.com" To: CCL Subject: CCL: Crystal Structure vs optimized structure Message-Id: <-42022-100529150415-24658-9Sgg2X4IGwvJqWm9f7XmDA_._server.ccl.net> X-Original-From: William Flak Content-Type: multipart/alternative; boundary="0-2063754023-1275159807=:20822" Date: Sat, 29 May 2010 12:03:27 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: William Flak [williamflak^-^yahoo.com] --0-2063754023-1275159807=:20822 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr. RadoslawThanks for your reply. I read your comment dated 2008.High= level of calculation means MP2/6-311++G**, it consumes a lot of time and I= want to test a tens of molecules, also most of them didn't optimize to the= crystal structure.Let me ask you again, May I do my calculation on the cry= stal structure without optimization? Could you support me with a=A0literatu= re=A0done this approach, please?Thanks in advance.W. Flak --- On Fri, 5/28/10, Radoslaw Kaminski rkaminski.rk-#-gmail.com wrote: > From: Radoslaw Kaminski rkaminski.rk-#-gmail.com Subject: CCL: Crystal Structure vs optimized structure To: "Flak, William " Date: Friday, May 28, 2010, 12:53 PM Hi William, I don't really get the point why are you worried. Of course you can do it. = However, you have to remember that such approach will lead to neglecting of= intermolacular interactions, and crystal field in general. If you look in = archive I was commenting on this some time ago (a year or so). The think I = could suggest to do is to take the best possible coordinates from the cryst= al (preferably from high-resolution measurement), keep the heavy atoms cons= tant and optimize hydrogen atom positions. Also, if you look at the literat= ure these could lead to different interaction energies (because the system = is relaxed or not etc.). Always take care while analysing the results! =0A Short question: what does it mean "high level" for you? Hope this helps somehow. Cheers, Radek 2010/5/28 William Flak williamflak---yahoo.com =0A =0ASent to CCL by: "William =A0Flak" [williamflak]^[yahoo.com] =0ADear CCL =0AI was wondering if I can calculate an interaction properties between two =0Amolecules based on crystal structure without optimization? Optimization = with =0Ahigh level couldn't give me the crystal structure. =0AAny comment would be appreciated. =0AW. Flak =0A =0A =0A =0A-=3D This is automatically added to each message by the mailing script = =3D- =0A =0AE-mail to subscribers: CHEMISTRY#ccl.net or use: =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0AE-mail to administrators: CHEMISTRY-REQUEST#ccl.net or use =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0A=0A =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A =0A=0A =0A=0A=0A =0A=0A =0A =A0 =A0 =A0http://www.ccl.net/spammers.txt =0A =0A=0A =0A =0A =0A=0A=0A=0A --0-2063754023-1275159807=:20822 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dr. Radoslaw
Thanks for your reply. = I read your comment dated 2008.
High level of calculation means M= P2/6-311++G**, it consumes a lot of time and I want to test a tens of molec= ules, also most of them didn't optimize to the crystal structure.
Let me ask you again, May I do my calculation on the crystal structure = without optimization? Could you support me with a literature = done this approach, please?
Thanks in advance.
W. Flak<= br>
--- On Fri, 5/28/10, Radoslaw Kaminski rkaminski.rk-#-gmail.com <= i><owner-chemistry:_:ccl.net> wrote:
Date: Friday, Ma= y 28, 2010, 12:53 PM

Hi William,

I d= on't really get the point why are you worried. Of course you can do it. How= ever, you have to remember that such approach will lead to neglecting of in= termolacular interactions, and crystal field in general. If you look in arc= hive I was commenting on this some time ago (a year or so). The think I cou= ld suggest to do is to take the best possible coordinates from the crystal = (preferably from high-resolution measurement), keep the heavy atoms constan= t and optimize hydrogen atom positions. Also, if you look at the literature= these could lead to different interaction energies (because the system is = relaxed or not etc.). Always take care while analysing the results!
=0A<= br>Short question: what does it mean "high level" for you?

Hope this= helps somehow.

Cheers,

Radek


2010/5/28 William Flak williamflak---yahoo.com <owner-chemi= stry#ccl.net>
=0A

=0ASent to CCL by: "William  Flak" [williamflak]^[yahoo.com= ]
=0ADear CCL
=0AI was wondering if I can calculate an interaction pr= operties between two
=0Amolecules based on crystal structure without opt= imization? Optimization with
=0Ahigh level couldn't give me the crystal = structure.
=0AAny comment would be appreciated.
=0AW. Flak
=0A
= =0A
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=0A=0A --0-2063754023-1275159807=:20822-- From owner-chemistry@ccl.net Sat May 29 15:49:00 2010 From: "Bill Ross ross**cgl.ucsf.edu" To: CCL Subject: CCL: Crystal Structure vs optimized structure Message-Id: <-42023-100529142721-11778-D5Xbr2dKxWzVT9JZE8IaRg###server.ccl.net> X-Original-From: Bill Ross Date: Sat, 29 May 2010 11:27:15 -0700 Sent to CCL by: Bill Ross [ross[A]cgl.ucsf.edu] > I was wondering if I can calculate an interaction properties between two > molecules based on crystal structure without optimization? Optimization > with > high level couldn't give me the crystal structure. > Any comment would be appreciated. What properties do you want? One might energy minimize in order to avoid trivially higher energy due to difference with the force field used for the xtal calculation. But beyond that, one might want to use e.g. molecular dynamics to explore the situation in more detail. Note that molecular mechanical energies are generally only good for comparing different configurations of a given chemical system. Bill From owner-chemistry@ccl.net Sat May 29 21:30:00 2010 From: "Radoslaw Kaminski rkaminski.rk^-^gmail.com" To: CCL Subject: CCL:G: Crystal Structure vs optimized structure Message-Id: <-42024-100529212349-23752-uUisTt9BVjBRr6nQmwBD1g+*+server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=000e0cd1e83ef3aef60487c596c0 Date: Sat, 29 May 2010 21:23:37 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk^-^gmail.com] --000e0cd1e83ef3aef60487c596c0 Content-Type: text/plain; charset=ISO-8859-1 Hi William, Well, in my opinion MP2/6-311++G** is not the highest level. I thought you think about something like Coupled Cluster or CI methods with huge basis sets. However, on the other hand, your level, I think, it's quite good for your purposes. If you try use the fair good approximation I think you could try to mimic the crystal field effects in some way. Quite good and simple method is the one proposed by Mark Spackman by finding averaged electric field around the molecule by the iterative approach. Usually it converges about 5-7 cycles. The method is applied for dipole moments and it's described here: M. A. Spackman et al., Chem. Phys. Lett., 2007, 443, 87 ; and for recent example see: D. Jayatilaka, Phys. Chem. Chem. Phys, 2009, 11, 7209. Also you can play with ONIOM approach. It's implemented in Gaussian but I never played with it so I can't provide useful references. I see Bill also suggested it before. The thing you should, in my opinion, at least do is to standardize X-H distances to neutron distances taken from literature if you really don't want to optimize the geometry or even the X-H positions. Also it depends how quality your X-ray (?) data is. From high-resolution data you're almost able to determine H atom positions and directions. Also you have to remember that you neglect some crystal field effects, and so even if it would be a dimer taken straight from the crystal - energies could be somehow comparable to another calculations or experiments. Or they could show some realistic trend. Also, I'm not a theoretician but a crystallographer so my view how to do something extremely accurate is probably a little bit different:) Hope this helps :) All the best, Radek PS. I'm not a Dr. and still far away to be one:P 2010/5/29 William Flak williamflak__yahoo.com > Dear Dr. Radoslaw > Thanks for your reply. I read your comment dated 2008. > High level of calculation means MP2/6-311++G**, it consumes a lot of time > and I want to test a tens of molecules, also most of them didn't optimize to > the crystal structure. > Let me ask you again, May I do my calculation on the crystal structure * > without* optimization? Could you support me with a literature done this > approach, please? > Thanks in advance. > W. Flak > > --- On *Fri, 5/28/10, Radoslaw Kaminski rkaminski.rk-#-gmail.com . ccl.net>* wrote: > > > From: Radoslaw Kaminski rkaminski.rk-#-gmail.com ccl.net> > Subject: CCL: Crystal Structure vs optimized structure > To: "Flak, William " > Date: Friday, May 28, 2010, 12:53 PM > > Hi William, > > I don't really get the point why are you worried. Of course you can do it. > However, you have to remember that such approach will lead to neglecting of > intermolacular interactions, and crystal field in general. If you look in > archive I was commenting on this some time ago (a year or so). The think I > could suggest to do is to take the best possible coordinates from the > crystal (preferably from high-resolution measurement), keep the heavy atoms > constant and optimize hydrogen atom positions. Also, if you look at the > literature these could lead to different interaction energies (because the > system is relaxed or not etc.). Always take care while analysing the > results! > > Short question: what does it mean "high level" for you? > > Hope this helps somehow. > > Cheers, > > Radek > > > 2010/5/28 William Flak williamflak---yahoo.com > > > >> >> Sent to CCL by: "William Flak" [williamflak]^[yahoo.com] >> Dear CCL >> I was wondering if I can calculate an interaction properties between two >> molecules based on crystal structure without optimization? Optimization >> with >> high level couldn't give me the crystal structure. >> Any comment would be appreciated. >> W. Flak>> >> E-mail to subscribers: CHEMISTRY#ccl.netor use:>> >> E-mail to administrators: CHEMISTRY-REQUEST#ccl.netor use>> >> >> > > --000e0cd1e83ef3aef60487c596c0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi William,

Well, in my opinion MP2/6-311++G** is not the highest le= vel. I thought you think about something like Coupled Cluster or CI methods= with huge basis sets. However, on the other hand, your level, I think, it&= #39;s quite good for your purposes.

If you try use the fair good approximation I think you could try to mim= ic the crystal field effects in some way. Quite good and simple method is t= he one proposed by Mark Spackman by finding averaged electric field around = the molecule by the iterative approach. Usually it converges about 5-7 cycl= es. The method is applied for dipole moments and it's described here: M= . A. Spackman et al., Chem. Phys. Lett., 2007, 443, 87 ; and for recent exa= mple see: D. Jayatilaka, Phys. Chem. Chem. Phys, 2009, 11, 7209.

Also you can play with ONIOM approach. It's implemented in Gaussian= but I never played with it so I can't provide useful references. I see= Bill also suggested it before.

The thing you should, in my opinion,= at least do is to standardize X-H distances to neutron distances taken fro= m literature if you really don't want to optimize the geometry or even = the X-H positions. Also it depends how quality your X-ray (?) data is. From= high-resolution data you're almost able to determine H atom positions = and directions.

Also you have to remember that you neglect some crystal field effects, = and so even if it would be a dimer taken straight from the crystal - energi= es could be somehow comparable to another calculations or experiments. Or t= hey could show some realistic trend. Also, I'm not a theoretician but a= crystallographer so my view how to do something extremely accurate is prob= ably a little bit different:)

Hope this helps :)

All the best,

Radek

PS. I'm= not a Dr. and still far away to be one:P


2010/5/29 William Flak willi= amflak__yahoo.com <owner-chemistry(0)ccl.net>
Dear Dr. Radoslaw
Thanks for your reply. I read your comment dated 2008= .
High level of calculation means MP2/6-311++G**, it consumes a l= ot of time and I want to test a tens of molecules, also most of them didn&#= 39;t optimize to the crystal structure.
Let me ask you again, May I do my calculation on the crystal structure= without optimization? Could you support me with a=A0literature=A0do= ne this approach, please?
Thanks in advance.
W. Flak
--- On Fri, 5/28/10, Radoslaw Kaminski rkaminski.rk-#-gmail.com <owner-chemistry . ccl.net> wrote:

From: Radoslaw Kaminski rkaminski.rk-#-gmail.com <owner-chemistry . ccl.net>
Subject: CCL: Crystal Structure vs = optimized structure
To: "Flak, William " <williamflak . yahoo.com>
Date: Friday, May 28, 2010, 12:53 PM=

Hi William,

I don't really get th= e point why are you worried. Of course you can do it. However, you have to = remember that such approach will lead to neglecting of intermolacular inter= actions, and crystal field in general. If you look in archive I was comment= ing on this some time ago (a year or so). The think I could suggest to do i= s to take the best possible coordinates from the crystal (preferably from h= igh-resolution measurement), keep the heavy atoms constant and optimize hyd= rogen atom positions. Also, if you look at the literature these could lead = to different interaction energies (because the system is relaxed or not etc= .). Always take care while analysing the results!

Short question: what does it mean "high level" for you?
Hope this helps somehow.

Cheers,

Radek


2010/5/28 William Flak william= flak---yahoo.com <owner-chemist= ry#ccl.net>

Sent to CCL by: "William =A0Flak" [williamflak]^[yahoo.com]
Dear CCL
I was wondering if I can calculate an interaction properties between two molecules based on crystal structure without optimization? Optimization wit= h
high level couldn't give me the crystal structure.
Any comment would be appreciated.
W. Flak




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--000e0cd1e83ef3aef60487c596c0-- From owner-chemistry@ccl.net Sat May 29 23:44:00 2010 From: "Brunsteiner, Michael micb : uic.edu" To: CCL Subject: CCL: how to build the protein loop Message-Id: <-42025-100529191823-23883-PJpMzn5Tti3FjWnDhQadBg-,-server.ccl.net> X-Original-From: "Brunsteiner, Michael" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 29 May 2010 18:18:03 -0500 MIME-Version: 1.0 Sent to CCL by: "Brunsteiner, Michael" [micb[#]uic.edu] you can use modeller for that (http://www.salilab.org/modeller) but i agree with Soaring Bear, modeling a stretch of 50 residues > from scratch will most likely give you a random result - remember, the fact that its structure is not well defined is basically the very definition of a loop! I'd leave these residues out altogether, replacing the dangling bonds on each end by C or N termini. Alternatively you can constrain the portion of the protein with known structure, and then do MD or MC simulation beginning with different starting structures for the loop (as suggested e.g. from modeller) ... but of course you will not get a definitive answer from that ... what you are likely to see then is wide range of possible structures, an ensemble if you like, but this ensemble will certainly not be complete. whether this can give you anything useful depends on what you want to learn from the simulation. for what its worth, mic On Thu, May 27, 2010 08:13, jeffle07 jeffle07[]163.com wrote: > Dear all, > We are going to build a protein model for MD simulation. But > several loop regions (about 50 residues in each missed loop) are > missed in the crystal structure. Could someone know how to build > these regions properly? Is there any package or webserver that can > do the job? > > Many thanks. > > Jeff. Yang