From owner-chemistry@ccl.net Wed Sep 30 00:08:00 2009 From: "yan liang ren yanliangren04~!~gmail.com" To: CCL Subject: CCL: how to fixed dihedral angle for amber md Message-Id: <-40378-090929234053-24654-WX+Gj2xr7YtQDCsHIKW0fQ() server.ccl.net> X-Original-From: "yan liang ren" Date: Tue, 29 Sep 2009 23:40:49 -0400 Sent to CCL by: "yan liang ren" [yanliangren04__gmail.com] Dear all, I went fixed some dihedral angle, when I do MD by using the amber 8. what can I do or how to set input file, hope some detailed answer. thanks very much! Best Regards! From owner-chemistry@ccl.net Wed Sep 30 01:26:01 2009 From: "Duy Le ttduyle**gmail.com" To: CCL Subject: CCL: external electric field in VASP 4.6 Message-Id: <-40379-090930012128-25355-JrI6RUigVRAaLU7s7WzPxg(!)server.ccl.net> X-Original-From: Duy Le Content-Type: multipart/alternative; boundary=001485f778104f13d40474c3fdac Date: Wed, 30 Sep 2009 00:30:04 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle%gmail.com] --001485f778104f13d40474c3fdac Content-Type: text/plain; charset=ISO-8859-1 You could use a function call "cache" from google search to reach the "unreachable text" On Tue, Sep 29, 2009 at 1:04 PM, Jose M Orts jm.orts]*[ua.es < owner-chemistry%ccl.net> wrote: > > Sent to CCL by: "Jose M Orts" [jm.orts:ua.es] > I am interested in making calculations in VASP 4.6, applying an external > electric field. It seems that the code allows this, but the relevant > keywords (tags) to be included in the INCAR file are not detailed in the > VASP manual. Some posts seem to exist at VASP forum,(related to EFIELD) but > the text of these seems to be unreachable (VASP forum not functioning, or > discontinued?). > I will appreciate any help on this point. > > JMOrts > Departamento de Qumica Fsica > Universidad de Alicante> > > -- -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. --001485f778104f13d40474c3fdac Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You could use a function call "cache" from google search to reach= the "unreachable text"

On Tue,= Sep 29, 2009 at 1:04 PM, Jose M Orts jm.orts]*[ua= .es <ow= ner-chemistry%ccl.net> wrote:

Sent to CCL by: "Jose M Orts" [jm.orts:ua.es]
I am interested in making calculations in VASP 4.6, applying an external el= ectric field. It seems that the code allows this, but the relevant keywords= (tags) to be included in the INCAR file are not detailed in the VASP manua= l. Some posts seem to exist at VASP forum,(related to EFIELD) but the text = of these seems to be unreachable (VASP forum not functioning, or discontinu= ed?).
I will appreciate any help on this point.

JMOrts
Departamento de Qumica Fsica
Universidad de Alicante



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY%ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST%ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
-----------------------= ---------------------------
Duy Le
PhD Student
Department of Physi= cs
University of Central Florida.
--001485f778104f13d40474c3fdac-- From owner-chemistry@ccl.net Wed Sep 30 06:34:00 2009 From: "Gerhard Goldbeck-Wood gerhard(~)accelrys.com" To: CCL Subject: CCL: Software for polymer MD simulations Message-Id: <-40380-090930062906-28403-hALsTO8mydhbJ0/uuACf7Q!A!server.ccl.net> X-Original-From: Gerhard Goldbeck-Wood Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 30 Sep 2009 05:28:37 -0400 MIME-Version: 1.0 Sent to CCL by: Gerhard Goldbeck-Wood [gerhard~~accelrys.com] Pablo, You could do all of these things using Materials Studio, which also offers good forcefields for polymers. In particular, the Materials Visualiser supports building random copolymers= . http://accelrys.com/products/materials-studio/ Regards Gerhard Dr Gerhard Goldbeck-Wood DIRECTOR, MATERIALS STUDIO MARKETING Accelrys, Ltd. 334 Cambridge Science Park Cambridge CB4 0WN, UK -----Original Message----- > From: owner-chemistry+gerhard=3D=3Daccelrys.com^ccl.net [mailto:owner-chemi= stry+gerhard=3D=3Daccelrys.com^ccl.net] On Behalf Of Pablo Englebienne p.en= glebienne-#-tue.nl Sent: 29 September 2009 15:10 To: Gerhard Goldbeck-Wood Subject: CCL: Software for polymer MD simulations Sent to CCL by: Pablo Englebienne [p.englebienne(!)tue.nl] Hi all, As a recent mover from the field of biomolecular to materials simulations, I would like to request your input to ease this transition. I am looking to perform atomistic simulations (MD, MC) of synthetic polymers and co-polymers. Reviewing the literature, it is hard to decide a simulation engine/force field combination. I am currently looking at GROMACS, NAMD, LAMMPS and DL_POLY, for reasons of available local expertise (GROMACS, NAMD) and apparent suitability for materials (LAMMPS, DL_POLY). There is not a definite choice, however. I would appreciate receiving comments/suggestions about these options, as well as others I might be overlooking. I am also looking for a program to construct initial coordinates of a random copolymer, if there was something like that ever coded. Optimally, I would like to be able to have structures of monomers (in some format), their relative ratio in the polymer and the chain length as input, and have coordinates (in some format) for the polymer as output. I am willing to wrap something together myself, but I was curious if there was a tool out there to do it. Kind regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven Univeristy of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtAccelrys Limited (http://accelrys.com) Registered office: 334 Cambridge Science Park, Cambridge, CB4 0WN, UK Registered in England: 2326316 From owner-chemistry@ccl.net Wed Sep 30 09:56:01 2009 From: "Werner K werner.schroedinger(~)googlemail.com" To: CCL Subject: CCL: Drug design book Message-Id: <-40381-090930090124-31780-oGuO15V1E9bplrR8YGqk2Q*server.ccl.net> X-Original-From: "Werner K" Date: Wed, 30 Sep 2009 09:01:20 -0400 Sent to CCL by: "Werner K" [werner.schroedinger_._googlemail.com] Hi, I am looking for a good reference book or web source of information for Drug Design. With this I mean, once I use software for virtual screening, how to be able to understand the interactions betweem the ligand and the protein, and how to determine or undersatnd what would be the modifications that would lead to drugs or better ligands. Thanks From owner-chemistry@ccl.net Wed Sep 30 12:37:01 2009 From: "Ol Ga eurisco1|*|pochta.ru" To: CCL Subject: CCL:G: Gaussian calculation problem Message-Id: <-40382-090930054931-25118-kSKO6enKpedwKe585aHRQA###server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 30 Sep 2009 05:49:28 -0400 Sent to CCL by: "Ol Ga" [eurisco1|*|pochta.ru] Dear Dr. Marta JUHASZ, First, the opportunity to create input files by using GV is very strict. So, you need to correct/add additional keywords by manual. Second, I played a lot with UGBS family of basis sets (I tried basis sets from bare UGBS to dressed by (1,2,3)P functions, with IOPs of Gaussian). However, I got the same error message. Hence, I suggest you to change your choice of basis set - I suppose Alrichs (all-electronic) basis sets like SVP, TZV etc. are better for your calculations than UGBS. Third, I guess you will get more errors with AIM sub-routine in Gaussian . :-) . It is not very stable. But if you are a lucky person ... :-) BTW. You can try a route section: # opt freq b3lyp/ugbs int=finegrid geom=connectivity aim=all Sincerely, Ol Ga ************************************** Dear Madame/Sir, I use the windows based Gaussian (Gaussian03W) and I would like to make calculation on a molecule at DFT level, using Bader's atoms in molecules (AIM) theory. As I know AIM does not with core potential basis sets. So I used an all electron basis set for the whole Cisplatin molecule. I checked Gaussian 03 Manual and I found only one basis set UGBS(1,2,3)P which is defined also on Pt and does not contain ECP. I tried the caluclation using UGBS bais set for each element (H, N, Cl and Pt). That is true that this UGBS is written in the Gaussian 03 Manual book, but it is not in the program (in the GaussView when I want to choose the theory level and basis set, this UGBS can not be found there as a option, but I typed this). So the route section was: # opt freq b3lyp/ugbs geom=connectivity aim=all and the Gaussian started but 8 minutes later it stoped and the next error message was appeared: No special actions if energy rises. Defaulting to unpruned grid for atomic number 78. Spurious integrated density or basis function: NE= 132 NElCor= 0 El error=2.40D-04 rel=1.82D-06 Tolerance=1.00D-03 Shell 1 absolute error=1.00D+00 Tolerance=1.20D-02 Shell 6 signed error=7.38D-01 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. The absolute error is bigger than the tolerance value what I do not know how to decrease. I also tried use UGBS1P basis set but this calculation requires higher memory what I have on the computer. Would you be so nice to tell me what can be the problem and how I can solve it? Thank you very much in advance. Sincerely, Dr. Marta JUHASZ Meisei University Department of Chemistry JAPAN From owner-chemistry@ccl.net Wed Sep 30 14:01:00 2009 From: "glinca:staff.uni-marburg.de" To: CCL Subject: CCL: Drug design book Message-Id: <-40383-090930120037-25686-bzQCqE8FTruU3rS6kyKiyQ(a)server.ccl.net> X-Original-From: glinca-.-staff.uni-marburg.de Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 30 Sep 2009 17:29:32 +0200 MIME-Version: 1.0 Sent to CCL by: glinca-x-staff.uni-marburg.de Hi, I found following book very helpful when I recently started my phd. "Molecular Recognition in Protein-Ligand Interactions: From Molecular =20 Recognition to Drug Design" It helped me to understand what are the differences between =20 programmes, what are they "doing" and which programmes it most =20 suitable for my target (keyword: training set). First chapter is a =20 very good introduction to applications that are available. Not too =20 much theory; pragmatic aspects are described. Latter chapters =20 concentrate on different aspects of protein-ligand interactions. There =20 is a goole book preview. There is a great book on drug design, but it is only available (still) =20 in German (Klebe, "Wirkstoffdesign", 2.te Auflage). Furthermore, I would suggest the homepage of Hugo Kubinyi. There are =20 many lecture slides that can be downloaded. But this is also the =20 disadvantage, very little text. Best regards, Serghei Zitat von "Werner K werner.schroedinger(~)googlemail.com" =20 : > > Sent to CCL by: "Werner K" [werner.schroedinger_._googlemail.com] > Hi, > > I am looking for a good reference book or web source of information =20 > for Drug Design. With this I mean, once I use software for virtual =20 > screening, how to be able to understand the interactions betweem the =20 > ligand and the protein, and how to determine or undersatnd what =20 > would be the modifications that would lead to drugs or better ligands. > > Thanks > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Wed Sep 30 18:20:01 2009 From: "Kadir Diri kadir[a]visual1.chem.pitt.edu" To: CCL Subject: CCL: And now something completely different: Part II Message-Id: <-40384-090930181748-28596-bIRb1jAh3xeH9yK847HGVA^server.ccl.net> X-Original-From: Kadir Diri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 30 Sep 2009 15:16:34 -0700 MIME-Version: 1.0 Sent to CCL by: Kadir Diri [kadir~!~visual1.chem.pitt.edu] Dear Friends and Colleagues, Our second film called "Laser" is out: http://www.youtube.com/watch?v=fhiOQSc5n90 In case you missed the first film explaining interaction of molecules with light using non-traditional visualization tools, here is the link: "Shine a light": http://www.youtube.com/watch?v=ceoO18RTiZI Enjoy and share! If you want to learn more about the production and/or share your thoughts, here are blog posts by the film director Professor Clifford Johnson: http://asymptotia.com/2009/09/14/laser/ http://asymptotia.com/2009/08/07/shine-a-light/ Trailers are fun too: http://www.youtube.com/watch?v=eJDe-OEfcLg http://www.youtube.com/watch?v=xYjoEvRpVbI&feature=video_response Brought to you by PeoplePixels and iOpenShell. --------------- Kadir Diri, PhD Research Scientist Department of Chemistry and iOpenShell Center SSC #401 University of Southern California Los Angeles, CA 90089-0482 -------------------------- Relativistic correction to Murphy's law: Whether things can go wrong or not, depends on your frame of reference. From owner-chemistry@ccl.net Wed Sep 30 22:05:00 2009 From: "Soaring Bear soaringbear[-]yahoo.com" To: CCL Subject: CCL: Drug design book Message-Id: <-40385-090930184023-4865-JpMPgdbZ2G8habh+z+wiIQ---server.ccl.net> X-Original-From: Soaring Bear Content-Type: text/plain; charset=us-ascii Date: Wed, 30 Sep 2009 14:40:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Soaring Bear [soaringbear,,yahoo.com] Richard Silverman The Organic Chemistry of Drug Design and Drug Action Soaring Bear Ph.D. Pharmacology soaringbear at yahoo.com http://soaringbear.com/nature/WeedsforNeeds.html http://www.nlm.nih.gov/mesh/presentations/bear_2005_aug/index.htm author of http://HerbMed.org & http://HerbInsight.com --- On Wed, 9/30/09, Werner K werner.schroedinger(~)googlemail.com wrote: > I am looking for a good reference book or web source of > information for Drug Design. With this I mean, once I use > software for virtual screening, how to be able to understand > the interactions betweem the ligand and the protein, and how > to determine or undersatnd what would be the modifications > that would lead to drugs or better ligands.