From owner-chemistry@ccl.net Tue Jul 16 01:06:01 2013 From: "Juan Manuel mayerzmytm#%#gmail.com" To: CCL Subject: CCL:G: Finding the transition state Message-Id: <-48956-130715121337-27704-MKqyVDvBb2Ze/bMvKgkMDw(0)server.ccl.net> X-Original-From: Juan Manuel Content-Type: multipart/alternative; boundary=001a11c2f63a41a7c304e18f24f5 Date: Mon, 15 Jul 2013 11:13:11 -0500 MIME-Version: 1.0 Sent to CCL by: Juan Manuel [mayerzmytm#,#gmail.com] --001a11c2f63a41a7c304e18f24f5 Content-Type: text/plain; charset=ISO-8859-1 Hello Ailar, I have not a lot of experience working with theoretical methods, but something that worked to me in order to find transition structure is use the berny method (only TS initial guess needed) with the keyword NoEigenTest, otherwise I found this process very dificult opt=(ts,noeigentest)....... best Juan Manuel Arce 2013/7/12 Ailar Badri ailar121242363:-:yahoo.co.uk > > Sent to CCL by: "Ailar Badri" [ailar121242363-.-yahoo.co.uk] > Dear CCLers, > > I'm looking for transition state structure using qst2 command, but I have > not been succeed so far. I tried many kinds of reactant/product structures > to find the transition state. However, my calculations always terminate > with the following error almost immediately after submitting the job: > > Old curvilinear step not converged, using linear step: > SCX= 2.80D+01 DXMaxT= 5.30-317 SCLim= 0.00D+00 Fact= 0.00D+00 > RedCar/ORedCr failed for GTrans. > Error termination via Lnk1e in /afs/ > ics.muni.cz/software/g09-D01/em64t.sse4.2/g09/l101.exe at Fri Jul 12 > 15:31:42 2013. > > I would be grateful if someone can help me. I am using Gaussian 09 rev. > D01. > > Regards, > Ailar Badri> > > --001a11c2f63a41a7c304e18f24f5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello Ailar,

I have not a lot of experi= ence working with theoretical methods, but something that worked to me in o= rder to find transition structure is use the berny method (only TS initial = guess needed) with the keyword NoEigenTest, otherwise I found this process = very dificult

opt=3D(ts,noeigentest).......

= best

Juan Manuel Arce


2013/7/12 Ailar Badri ailar121242363= :-:yahoo.co.uk <owner-chemistry###c= cl.net>

Sent to CCL by: "Ailar =A0Badri" [ailar121242363-.-yahoo.co.uk]
Dear CCLers,

I'm looking for transition state structure using qst2 command, but I ha= ve not been succeed so far. I tried many kinds of reactant/product structur= es to find the transition state. However, my calculations always terminate = with the following error almost immediately after submitting the job:

Old curvilinear step not converged, using linear step:
=A0SCX=3D 2.80D+01 DXMaxT=3D 5.30-317 SCLim=3D 0.00D+00 Fact=3D 0.00D+00 =A0RedCar/ORedCr failed for GTrans.
=A0Error termination via Lnk1e in /afs/ics.muni.cz/softwar= e/g09-D01/em64t.sse4.2/g09/l101.exe at Fri Jul 12 15:31:42 2013.

I would be grateful if someone can help me. I am using Gaussian 09 rev. D01= .

Regards,
Ailar Badri



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--001a11c2f63a41a7c304e18f24f5-- From owner-chemistry@ccl.net Tue Jul 16 04:23:01 2013 From: "Jamie Platts platts.:.cf.ac.uk" To: CCL Subject: CCL: MGMS Silver Jubilee Prize Message-Id: <-48957-130716042159-19676-QAooQ84a8tchHjkmE0PvWw]*[server.ccl.net> X-Original-From: "Jamie Platts" Date: Tue, 16 Jul 2013 04:21:57 -0400 Sent to CCL by: "Jamie Platts" [platts*_*cf.ac.uk] Dear CCL We are pleased to announce that the 2013 round of the MGMS Silver Jubilee Prize will be awarded to Dr. Lynn Kamerlin of Uppsala University, in recognition of her outstanding contributions to a wide range of computational chemistry and biophysics. Jamie Platts, on behalf of the MGMS Board of Trustees From owner-chemistry@ccl.net Tue Jul 16 08:00:00 2013 From: "Peter Damian Jarowski p.d.jarowski||surrey.ac.uk" To: CCL Subject: CCL: Platinum with ECPs in Molpro Message-Id: <-48958-130716074245-8022-WJy+UJoSANc1C++D5LzL0Q%server.ccl.net> X-Original-From: "Peter Damian Jarowski" Date: Tue, 16 Jul 2013 07:42:44 -0400 Sent to CCL by: "Peter Damian Jarowski" [p.d.jarowski,,surrey.ac.uk] Dear CCLers: Does anyone have a sample input file example for Molpro in which they have calculated a platinum complex using ECPS (either SDD or LANL)? Is there a standard setup for doing this where the core electrons and angular momenta can be set without additional information/knowledge. The platinum atom is +2, square planar. I would like to perform some excited state calculations, ultimately it would be nice to do some spin-orbit calculations. The input I have tried is this. basis={ spdf,C,VDZ;C; spdf,N,VDZ;C; sp,H,VDZ;C; ecp,Pt,ECP70MWB; spdfg,Pt,ECP70MWB;C; } Take into account that I am simply mimicking inputs I have found around, but don't yet exactly understand what I am doing. I believe I am choosing 70 core electrons to be modeled as pseudo- potentials for a neutral atom (already wrong perhaps as the Pt is +2) and WB for quasi-reletivistic. I have choses 70 because platinum is atomic number 78, in +2 leaving 6 electrons in the valence. Any and all help would be much appreciated. References to get a handle on the use of pseudo- potentials would also be great. Best Regards, Peter From owner-chemistry@ccl.net Tue Jul 16 08:45:00 2013 From: "Grant Hill Grant.Hill*_*glasgow.ac.uk" To: CCL Subject: CCL: Platinum with ECPs in Molpro Message-Id: <-48959-130716084033-28789-+4gZDyeX03a93fLVFd5IAQ]_[server.ccl.net> X-Original-From: Grant Hill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 16 Jul 2013 13:40:16 +0100 MIME-Version: 1.0 Sent to CCL by: Grant Hill [Grant.Hill{}glasgow.ac.uk] Dear Peter, It would probably be simplest to use the correlation consistent basis sets [1] here. For example: basis={ default,vdz,pt=vdz-pp } This replaces 60 electrons on Pt, with the 5sp orbitals treated with the frozen core approximation. Best regards, Grant [1] Figgen et al., J. Chem. Phys. 130, 164108 (2009) On 16 Jul 2013, at 12:42, Peter Damian Jarowski p.d.jarowski||surrey.ac.uk wrote: > > Sent to CCL by: "Peter Damian Jarowski" [p.d.jarowski,,surrey.ac.uk] > Dear CCLers: > > Does anyone have a sample input file example for Molpro in which they have calculated a platinum > complex using ECPS (either SDD or LANL)? Is there a standard setup for doing this where the core > electrons and angular momenta can be set without additional information/knowledge. The platinum > atom is +2, square planar. I would like to perform some excited state calculations, ultimately it > would be nice to do some spin-orbit calculations. The input I have tried is this. > > basis={ > spdf,C,VDZ;C; > spdf,N,VDZ;C; > sp,H,VDZ;C; > ecp,Pt,ECP70MWB; > spdfg,Pt,ECP70MWB;C; > } > > Take into account that I am simply mimicking inputs I have found around, but don't yet exactly > understand what I am doing. I believe I am choosing 70 core electrons to be modeled as pseudo- > potentials for a neutral atom (already wrong perhaps as the Pt is +2) and WB for quasi-reletivistic. I > have choses 70 because platinum is atomic number 78, in +2 leaving 6 electrons in the valence. > > Any and all help would be much appreciated. References to get a handle on the use of pseudo- > potentials would also be great. > > Best Regards, > > Peter> > From owner-chemistry@ccl.net Tue Jul 16 10:04:00 2013 From: "Errol Lewars elewars * trentu.ca" To: CCL Subject: CCL:G: Finding the transition state Message-Id: <-48960-130716091803-762-GecD1Y64ROHk456faDOk7w*o*server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Jul 2013 09:17:53 -0400 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars_+_trentu.ca] 2013 July 16 "I have not a lot of experience working with theoretical methods, but something that worked to me in order to find transition structure is use the berny method (only TS initial guess needed) with the keyword NoEigenTest, otherwise I found this process very dificult." I second that: I have *never* found that (otherwise good) method to work unless Opt is flagged with NoEigenTest; I suspect the need to add this is not generally known and is the cause of much trouble finding transition states. Try an input structure built using simply (?) chemical intuition. Try ratcheting up a TS from, say, rapid AM1 to the higher desired level . E. Lewars == Juan Manuel mayerzmytm#%#gmail.com wrote: > Hello Ailar, > > I have not a lot of experience working with theoretical methods, but > something that worked to me in order to find transition structure is > use the berny method (only TS initial guess needed) with the keyword > NoEigenTest, otherwise I found this process very dificult > > opt=(ts,noeigentest)....... > > best > > Juan Manuel Arce > > > 2013/7/12 Ailar Badri ailar121242363:-:yahoo.co.uk > > > > > Sent to CCL by: "Ailar Badri" [ailar121242363-.-yahoo.co.uk > ] > Dear CCLers, > > I'm looking for transition state structure using qst2 command, but > I have not been succeed so far. I tried many kinds of > reactant/product structures to find the transition state. However, > my calculations always terminate with the following error almost > immediately after submitting the job: > > Old curvilinear step not converged, using linear step: > SCX= 2.80D+01 DXMaxT= 5.30-317 SCLim= 0.00D+00 Fact= 0.00D+00 > RedCar/ORedCr failed for GTrans. > Error termination via Lnk1e in > /afs/ics.muni.cz/software/g09-D01/em64t.sse4.2/g09/l101.exe > at > Fri Jul 12 15:31:42 2013. > > I would be grateful if someone can help me. I am using Gaussian 09 > rev. D01. > > Regards, > Ailar Badri > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY]=[ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST]=[ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Tue Jul 16 10:56:01 2013 From: "Amy Austin amy_jean_austin*yahoo.com" To: CCL Subject: CCL:G: Finding the transition state Message-Id: <-48961-130716104810-25670-1ReyKP1JgkHXeavq04YZ0w=-=server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="1073417382-1168580134-1373986082=:56690" Date: Tue, 16 Jul 2013 07:48:02 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin^-^yahoo.com] --1073417382-1168580134-1373986082=:56690 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Juan, Have you tried a QST3? In addition to the reactants and products, = this will allow you to use input an initial guess for the transition state.= =0A=0AAdditionally, you could get an estimate of the reaction path using o= pt=3Dpath from the optimized reactant. The highest energy point along the p= ath can be used as an estimate for the transition state of the QST3 calc, w= hile the step down the gradient on the reactant side may be used as the rea= ctant guess in the QST3, and so on for the product.=0A=0AWhichever method y= ou use, I would run an IRC once you are finished to ensure the transition s= tate you've calculated is the for the reaction you intended. =0A=0AGood luc= k,=0A=0AAmy=0A=0A=0A=0A=0A________________________________=0A From: Juan Ma= nuel mayerzmytm#%#gmail.com =0ATo: "Austin, Amy J = " =0ASent: Monday, July 15, 2013 12:13 = PM=0ASubject: CCL:G: Finding the transition state=0A =0A=0A=0AHello Ailar,= =0A=0AI have not a lot of experience working with theoretical methods, but = something that worked to me in order to find transition structure is use th= e berny method (only TS initial guess needed) with the keyword NoEigenTest,= otherwise I found this process very dificult=0A=0Aopt=3D(ts,noeigentest)..= .....=0A=0Abest=0A=0AJuan Manuel Arce=0A=0A=0A=0A2013/7/12 Ailar Badri aila= r121242363:-:yahoo.co.uk =0A=0A=0A>Sent to CCL= by: "Ailar =A0Badri" [ailar121242363-.-yahoo.co.uk]=0A>Dear CCLers,=0A>=0A= >I'm looking for transition state structure using qst2 command, but I have = not been succeed so far. I tried many kinds of reactant/product structures = to find the transition state. However, my calculations always terminate wit= h the following error almost immediately after submitting the job:=0A>=0A>O= ld curvilinear step not converged, using linear step:=0A>=A0SCX=3D 2.80D+01= DXMaxT=3D 5.30-317 SCLim=3D 0.00D+00 Fact=3D 0.00D+00=0A>=A0RedCar/ORedCr = failed for GTrans.=0A>=A0Error termination via Lnk1e in /afs/ics.muni.cz/so= ftware/g09-D01/em64t.sse4.2/g09/l101.exe at Fri Jul 12 15:31:42 2013.=0A>= =0A>I would be grateful if someone can help me. I am using Gaussian 09 rev.= D01.=0A>=0A>Regards,=0A>Ailar Badri=0A>=0A>=0A>=0A>-=3D This is automatica= lly added to each message by the mailing script =3D-=0A>=0A>E-mail to subsc= ribers: CHEMISTRY]=3D[ccl.net or use:=0A>=A0 =A0 =A0 http://www.ccl.net/cgi= -bin/ccl/send_ccl_message=0A>=0A>E-mail to administrators: CHEMISTRY-REQUES= T]=3D[ccl.net or use=0A>=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl= _message=0A>=0A>Subscribe/Unsubscribe:=0A>=A0 =A0 =A0 http://www.ccl.net/ch= emistry/sub_unsub.shtml=0A>=0A>Before posting, check wait time at: http://w= ww.ccl.net=0A>=0A>Job: http://www.ccl.net/jobs=0A>Conferences: http://serve= r.ccl.net/chemistry/announcements/conferences/=0A>=0A>Search Messages: http= ://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A>=A0 =A0 =A0 http://ww= w.ccl.net/spammers.txt=0A>=0A>RTFI: http://www.ccl.net/chemistry/aboutccl/i= nstructions/=0A>=0A>=0A> --1073417382-1168580134-1373986082=:56690 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Juan, Have you tried a QST3? = In addition to the reactants and products, this will allow you to use input= an initial guess for the transition state.

Additionally, you could= get an estimate of the reaction path using opt=3Dpath from the optimized r= eactant. The highest energy point along the path can be used as an estimate= for the transition state of the QST3 calc, while the step down the gradien= t on the reactant side may be used as the reactant guess in the QST3, and s= o on for the product.

Whichever method you use, I would run an IRC o= nce you are finished to ensure the transition state you've calculated is th= e for the reaction you intended.

Good luck,

Amy


From: Juan Manuel mayerzmytm#%#gmail.com <owner-chemist= ry-#-ccl.net>
To: "Au= stin, Amy J " <amy_jean_austin-#-yahoo.com>
Sent: Monday, July 15, 2013 12:13 PM
= Subject: CCL:G: Finding t= he transition state

<= div id=3D"yiv9398552246">
Hello Ailar,

I= have not a lot of experience working with theoretical methods, but somethi= ng that worked to me in order to find transition structure is use the berny= method (only TS initial guess needed) with the keyword NoEigenTest, otherw= ise I found this process very dificult
=0A=0A

opt= =3D(ts,noeigentest).......

best

Juan Manuel Arce

2013/7/12 Ailar Badri ailar121242= 363:-:ya= hoo.co.uk <owner-chemistry]=3D[ccl.net>
=0A=0A
=0ASent to CCL by: "Ailar  Ba= dri" [ailar121242363-.-yahoo.co.uk]
=0ADear CCLers,
=0A
=0AI'm looking= for transition state structure using qst2 command, but I have not been suc= ceed so far. I tried many kinds of reactant/product structures to find the = transition state. However, my calculations always terminate with the follow= ing error almost immediately after submitting the job:
=0A=0A=0A
=0AO= ld curvilinear step not converged, using linear step:
=0A SCX=3D 2.= 80D+01 DXMaxT=3D 5.30-317 SCLim=3D 0.00D+00 Fact=3D 0.00D+00
=0A Re= dCar/ORedCr failed for GTrans.
=0A Error termination via Lnk1e in /= afs/ics.muni.cz/software/g09-D01/em64t.ss= e4.2/g09/l101.exe at Fri Jul 12 15:31:42 2013.
=0A
=0AI would be = grateful if someone can help me. I am using Gaussian 09 rev. D01.
=0A=0ARegards,
=0AAilar Badri
=0A
=0A
=0A
=0A-=3D This is auto= matically added to each message by the mailing script =3D-
=0A
=0AE-m= ail to subscribers: CHEMISTRY]=3D= [ccl.net or use:
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=0A
=0AE-mail to admini= strators: CHEMIST= RY-REQUEST]=3D[ccl.net or use
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=0AJob: http://www.ccl.net/jobs
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=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
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=0A


--1073417382-1168580134-1373986082=:56690-- From owner-chemistry@ccl.net Tue Jul 16 12:34:00 2013 From: "Hira zaidi s.hirabatool^-^ymail.com" To: CCL Subject: CCL: DCD file format Message-Id: <-48962-130716123206-15846-dWCGBnZuHzYd13yVFqurZQ-#-server.ccl.net> X-Original-From: "Hira zaidi" Date: Tue, 16 Jul 2013 12:32:05 -0400 Sent to CCL by: "Hira zaidi" [s.hirabatool,ymail.com] I am writing a python script to read dcd files.For that I want to know the exact format of a dcd file ( generated by NAMD or CHARMM).Please can anyone help me regarding this. Thanks, Hira Batool s.hirabatool*ymail.com From owner-chemistry@ccl.net Tue Jul 16 14:37:00 2013 From: "Lucus White lucus.white2000(~)gmail.com" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48963-130716142948-28674-BXf4oXJGMLJqud5nvITAFA/./server.ccl.net> X-Original-From: Lucus White Content-Type: multipart/alternative; boundary=047d7b45148a23335c04e1a52956 Date: Tue, 16 Jul 2013 14:29:42 -0400 MIME-Version: 1.0 Sent to CCL by: Lucus White [lucus.white2000__gmail.com] --047d7b45148a23335c04e1a52956 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I've received many replies. Thanks for all your replies. They are very helpful! Best wishes, Lucus On Fri, Jul 12, 2013 at 4:54 PM, shawn wong subchap.sp4]=[gmail.com < owner-chemistry!^!ccl.net> wrote: > You may use www.sciencing.net. You can add your own keywords and receive > email notifications when new papers are published. It's very convenient. > > Best wishes, > Shawn > > 2013/7/9 Lucus White lucus.white2000,gmail.com > > >> >>> >>> Sent to CCL by: "Lucus White" [lucus.white2000[]gmail.com] >>> Hi All, >>> >>> I'm just curious about what the best way is to check the latest papers. >>> For instance, I want to see the >>> most recent issues and the ASAP papers in the major journals. I normally >>> visit the journal websites one >>> by one, but is there any better way to do it? >>> >>> Any suggestions would be appreciated. >>> >>> Best wishes, >>> Lucus >>> lucus.white2000,,gmail.com* >>> * >>> E-mail to subscribers: CHEMISTRY\a/ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST\a/ccl.net or use>>> **>>> >>> >>> >> > --047d7b45148a23335c04e1a52956 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi All,

I've received many replies.= Thanks for all your replies. They are very helpful!

Best wishes,
Lucus

On Fri, Jul 12, 2013 at 4:54 PM, shawn wong subc= hap.sp4]=3D[gmail.com &l= t;owner-chemis= try!^!ccl.net> wrote:
You may use www.sciencing.net. You can= add your own keywords and receive email notifications when new papers are = published. It's very convenient.

Best wishes,
Shawn

2013/7/9 Lucus White lucus.white2000,gmail.com <owner-chemistry\a/ccl.net>=

Sent to CCL by: "Lucus =A0White" [lucus.white2000[]gmail.com]
Hi All,

I'm just curious about what the best way is to check the latest papers.= For instance, I want to see the
most recent issues and the ASAP papers in the major journals. I normally vi= sit the journal websites one
by one, but is there any better way to do it?

Any suggestions would be appreciated.

Best wishes,
Lucus
lucus.white2000,,gmail.com



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--047d7b45148a23335c04e1a52956-- From owner-chemistry@ccl.net Tue Jul 16 17:10:00 2013 From: "Andrew Dalke dalke%dalkescientific.com" To: CCL Subject: CCL: DCD file format Message-Id: <-48964-130716162645-17497-Ptl2tobLuBvaufR1Y79Dhw-*-server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 16 Jul 2013 22:26:37 +0200 Mime-Version: 1.0 (Apple Message framework v1283) Sent to CCL by: Andrew Dalke [dalke : dalkescientific.com] On Jul 16, 2013, at 6:32 PM, Hira zaidi s.hirabatool^-^ymail.com wrote: > I am writing a python script to read dcd files.For that I want to know the exact format of a dcd file ( generated by NAMD or CHARMM). The high-level description is available at http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html This defines the format using Fortran I/O, which is not the same as defining the byte layer. It's enough though that Mark Nelson, one of the original NAMD developers from the mid-1990s, used it and byte inspection of existing DCD files to write the low-level NAMD parser. Otherwise, that code is available as part of the NAMD and VMD distributions, so you can download the source code, inspect it for yourself, and use that to write your own parser. That's a bit overkill. Many people use NAMD's parser directly. For example, there's a Python module for reading MD trajectory files, which embeds the UIUC DCD reader. It's available from: https://code.google.com/p/mdanalysis/ You can install it with "pip install mdanalysis", if you have pip installed for your Python installation. Here's an example of working directly with a DCD file: >>> import MDAnalysis.coordinates >>> reader = MDAnalysis.coordinates.reader("/Users/dalke/ftps/vmd-1.0/proteins/alanin.DCD") >>> reader < DCDReader '/Users/dalke/ftps/vmd-1.0/proteins/alanin.DCD' with 100 frames of 66 atoms (0 fixed) > >>> for timestep in reader[:10]: # Get the first 10 time steps ... print timestep[0] # Information about the first atom index ... [-0.736 -3.08800006 2.98200011] [-0.90899998 -2.46199989 3.00300002] [-0.79799998 -2.10500002 3.27099991] [-0.54500002 -1.94000006 3.6559999 ] [-0.59799999 -1.36399996 3.75600004] [-0.40400001 -1.50399995 4.24900007] [-0.317 -1.81599998 4.46299982] [-1.12300003 -1.48599994 4.09600019] [-1.74600005 -0.97600001 3.62800002] [-2.0769999 -1.06799996 3.20700002] Regards, Andrew dalke**dalkescientific.com From owner-chemistry@ccl.net Tue Jul 16 20:04:00 2013 From: "Joshua Adelman jla65{=}pitt.edu" To: CCL Subject: CCL: DCD file format Message-Id: <-48965-130716130247-30533-UtyzUR6SapzlwoxqiAFInA~!~server.ccl.net> X-Original-From: Joshua Adelman Content-type: multipart/alternative; boundary=Apple-Mail-4-549970199 Date: Tue, 16 Jul 2013 13:02:41 -0400 MIME-version: 1.0 (Apple Message framework v1085) Sent to CCL by: Joshua Adelman [jla65]![pitt.edu] --Apple-Mail-4-549970199 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi Hira, There are a number of tools to read dcd coordinates into python. I would = check out the following libraries: https://github.com/rmcgibbo/mdtraj http://www.csb.pitt.edu/prody https://code.google.com/p/mdanalysis/ I also have used the python wrapping of VMD's molfile plugin included = in: http://www.deshawresearch.com/resources_timescapes.html Similar functionality through python is also in Desmond itself = (http://www.deshawresearch.com/resources_desmond.html), but I've found = it to be more difficult to build on several platforms. If you want to code a reader yourself, you could check out the source = code of any of the above libraries for hints, or take a look at: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html=20 although a lot of the links are broken on that page. Josh On Jul 16, 2013, at 12:32 PM, Hira zaidi s.hirabatool^-^ymail.com wrote: >=20 > Sent to CCL by: "Hira zaidi" [s.hirabatool,ymail.com] > I am writing a python script to read dcd files.For that I want to know = the exact format of a dcd file ( generated by NAMD or CHARMM).Please can = anyone help me regarding this. >=20 > Thanks, >=20 > Hira Batool > s.hirabatool%x%ymail.com >=20 >=20 >=20 > -=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>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail-4-549970199 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Hi = Hira,

There are a number of tools to read dcd = coordinates into python. I would check out the following = libraries:

http://www.csb.pitt.edu/prody

I also have used the python = wrapping of VMD's molfile plugin included in:

Similar functionality through python is also in Desmond itself (http://www.d= eshawresearch.com/resources_desmond.html), but I've found it to be = more difficult to build on several = platforms.

If you want to code a reader = yourself, you could check out the source code of any of the above = libraries for hints, or take a look at:

although a lot of the links are broken on = that = page.

Josh



On Jul 16, 2013, at 12:32 PM, Hira zaidi = s.hirabatool^-^ymail.com wrote:


Sent to CCL by: "Hira  zaidi" = [s.hirabatool,ymail.com]
I am writing a python script to read dcd = files.For that I want to know the exact format of a dcd file ( generated = by NAMD or CHARMM).Please can anyone help me regarding = this.

Thanks,

Hira = Batool
s.hirabatool%x%ymail.com



-=3D This is = automatically added to each message by the mailing script =3D-
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= --Apple-Mail-4-549970199-- From owner-chemistry@ccl.net Tue Jul 16 20:39:00 2013 From: "shanawersi shanawersi|upatras.gr" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48966-130716164008-19059-guIQ21pWCzveboQljYID1A^_^server.ccl.net> X-Original-From: shanawersi Content-Type: multipart/alternative; boundary="=_aa4356f9f4b4ad5e5fe58252d234186a" Date: Tue, 16 Jul 2013 23:39:58 +0300 MIME-Version: 1.0 Sent to CCL by: shanawersi [shanawersi*o*upatras.gr] --=_aa4356f9f4b4ad5e5fe58252d234186a Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Hi I found this link useful concerning the subject: http://www.compchemhighlights.org/ [11] Shani On 2013-07-16 21:29, Lucus White lucus.white2000(~)gmail.com wrote: > Hi All, > > I've received many replies. Thanks for all your replies. They are very helpful! > > Best wishes, > Lucus > > On Fri, Jul 12, 2013 at 4:54 PM, shawn wong subchap.sp4]=[gmail.com [1] wrote: > >> You may use www.sciencing.net [10]. You can add your own keywords and receive email notifications when new papers are published. It's very convenient. >> >> Best wishes, >> Shawn >> >>> 2013/7/9 Lucus White lucus.white2000,gmail.com [1] >>> >>>> Sent to CCL by: "Lucus White" [lucus.white2000[]gmail.com [1]] >>>> Hi All, >>>> >>>> I'm just curious about what the best way is to check the latest papers. For instance, I want to see the >>>> most recent issues and the ASAP papers in the major journals. I normally visit the journal websites one >>>> by one, but is there any better way to do it? >>>> >>>> Any suggestions would be appreciated. >>>> >>>> Best wishes, >>>> Lucus >>>> lucus.white2000,,gmail.com [1]>>>> E-mail to subscribers: CHEMISTRYa/ccl.net or use:[2] >>>> >>>> E-mail to administrators: CHEMISTRY-REQUESTa/ccl.net or use[2][3][4][5][6][7][8][9] Links: ------ [1] http://gmail.com [2][3][4] http://www.ccl.net [5] http://www.ccl.net/jobs [6] http://server.ccl.net/chemistry/announcements/conferences/ [7] http://www.ccl.net/chemistry/searchccl/index.shtml [8][9] http://www.ccl.net/chemistry/aboutccl/instructions/ [10] http://www.sciencing.net [11] http://www.compchemhighlights.org/ --=_aa4356f9f4b4ad5e5fe58252d234186a Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=UTF-8

Hi

I found this link useful concerning the subject:

http://www.compchemhighli= ghts.org/

 

Shani

 

On 2013-07-16 21:29, Lucus White lucus.white2000(~)gmail.com wrote:

Hi All,
 
I've received many replies. Thanks for all your replies. They are very= helpful!
 
Best wishes,
Lucus


On Fri, Jul 12, 2013 at 4:54 PM, shawn wong subc= hap.sp4]=3D[gmail.com <owner-chemistry%a%ccl.net>= wrote:
You may use www.sciencing.net= =2E You can add your own keywords and receive email notifications when new = papers are published. It's very convenient.
 
Best wishes,
Shawn

2013/7/9 Lucus White lucus.white2000,gmail.com <owner-chemistry\a/ccl.net>

Sent to CCL by: "Lucus &nb= sp;White" [lucus.white2000[]gmail.com]
Hi All,

I'm just curious about what the best way is to check= the latest papers. For instance, I want to see the
most recent issue= s and the ASAP papers in the major journals. I normally visit the journal w= ebsites one
by one, but is there any better way to do it?

= Any suggestions would be appreciated.

Best wishes,
Lucus=
lucus.white2000,,gmail.com


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