From owner-chemistry@ccl.net Sun May 10 05:11:00 2009 From: "Lukasz Cwiklik cwiklik%gmail.com" To: CCL Subject: CCL: molecular dynamic in water Message-Id: <-39266-090510050743-24643-nguazxSJBA0me9QGDqb06Q#server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 10 May 2009 12:00:01 +0300 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [cwiklik:_:gmail.com] Deat Veronique, As you stated, it seems that you have problems with interactions between your molecule and water molecules. Such interactions, generally, have two components: electrostatic & van der Waals. In order to properly describe them, one has to carefully and physically meaningful chose a proper values of their parameters (i.e., atomic charges & vdW parameters). Usually, you cannot play with electrostatic a lot so people try to fit van der Walls parameters. One of possible ways would be to fit them to reproduce ab initio potential energy surfaces for interactions between water and your molecule. An example of derivation of such intermolecular terms can be found in Al-Halbi et al, J. Phys. Chem. A 107 (2003) 10615. But you have to be careful here because you should not change well established TIP3P water vdW parameters, otherwise you can make your water behavior nonphysical. You should rather either play with your molecule's vdW or (if possible in Charmm) define additional terms for intermolecular vdW terms. Best, Lukasz --=20 Lukasz Cwiklik http://cwiklik.wordpress.com On Thu, May 7, 2009 at 6:11 PM, Veronique LEGRAND vflegrand**free.fr wrote: > > Sent to CCL by: "Veronique =A0LEGRAND" [vflegrand[-]free.fr] > > Hello everybody, > > I'm face to a problem. I defined the parameters and the topology of a mol= ecule (not a protein or a residue). I performed a molecular dynamic in gas = phase with Charmm, whihout any problem. But when I did the same thing in wa= ter, my molecule begins completly desorganized : the cycles are not plane s= hape any more... > I checked my files several times. > I have all the topology corresponding to water: > RESI TIP3 =A0 =A0 =A0 =A0 0.000 nodihedral > GROUP > ATOM OH2 =A0OT =A0 =A0 -0.834 > ATOM H1 =A0 HT =A0 =A0 =A00.417 > ATOM H2 =A0 HT =A0 =A0 =A00.417 > BOND OH2 H1 OH2 H2 H1 H2 > ANGLE H1 OH2 H2 > ACCEPTOR OH2 > PATCHING FIRS NONE LAST NONE > > I have all the parameters corresponding to water: > BONDS > OT =A0 HT =A0 =A0450.000 =A0 =A0 0.9572 > HT =A0 HT =A0 =A0 =A00.000 =A0 =A0 1.5139 > ANGLES > HT =A0 OT =A0 HT =A0 =A0 55.000 =A0 104.5200 > NONBONDED > OT =A0 =A0 0.000000 =A0-0.152100 =A0 =A0 1.768200 > HT =A0 =A0 0.000000 =A0-0.046000 =A0 =A0 0.224500 > > And I have all the topology and parameters of my molecule. The output of = dynamic doesn't tell me there is "MISSING PARAMETER" etc, it runs.. > > I suppose it's a problem of interaction between my molecule and water mol= ecule but I don't know how to introduce it. Actualy it's the non bonded par= ameters that manage it, and all my atoms are in the list. > > I think it's not something complicated but I don't find the key! > If you have any idea, I will read you with pleasure. > Thanks a lot. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Sun May 10 08:53:01 2009 From: "Edmanuel Torres e.torres .. mpie.de" To: CCL Subject: CCL: molecular dynamic in water Message-Id: <-39267-090510084824-17612-mcAaYAYvYpSnQu6EFFZcpQ__server.ccl.net> X-Original-From: "Edmanuel Torres" Content-Transfer-Encoding: quoted-printable Content-Transfer-Encoding: quoted-printable Content-type: text/plain; charset="utf-8" Content-Type: text/plain; charset="utf-8" Date: Sun, 10 May 2009 14:46:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Edmanuel Torres" [e.torres() mpie.de] Dear Veronique =2C Before to select the force field for the water molecules=2C make sure you k= now very well the properties of your molecule=2C things like ionic or dipol= e fields may result of a miss behaviour of the system if a inappropriate wa= ter model is used=2E Here some useful links=3A http=3A//en=2Ewikipedia=2Eorg/wiki/Force=5Ffield=5F=28chemistry=29 http=3A//en=2Ewikipedia=2Eorg/wiki/Water=5Fmodel http=3A//www=2Esklogwiki=2Eorg/SklogWiki/index=2Ephp/Category=3AModels http=3A//www=2Elsbu=2Eac=2Euk/water/models=2Ehtml Also before a full MD of the system=2C better run a MD for the water with t= he molecule fixed=2E It may be that the initial position of the water molec= ules are unrealistic=2E After the relaxation of the water you can run a ful= l MD of the system=2E Best=2C Edmanuel=20 ----- Original Message ----- > From=3A Veronique LEGRAND vflegrand**free=2Efr =5Bmailto=3Aowner-chemistry=40ccl=2Enet=5D To=3A Torres=2C Edmanuel -id=233in- =5Bmailto=3Ae=2Etorres=40mpie=2Ede=5D Sent=3A Thu=2C 07 May 2009 17=3A11=3A34 +0200 Subject=3A CCL=3A molecular dynamic in water //=20 // Sent to CCL by=3A =22Veronique LEGRAND=22 =5Bvflegrand=5B-=5Dfree=2Efr= =5D //=20 // Hello everybody=2C=20 //=20 // I=27m face to a problem=2E I defined the parameters and the topology of= a // molecule =28not a protein or a residue=29=2E I performed a molecular dyn= amic in // gas phase with Charmm=2C whihout any problem=2E But when I did the same= thing in // water=2C my molecule begins completly desorganized =3A the cycles are no= t plane // shape any more=2E=2E=2E // I checked my files several times=2E // I have all the topology corresponding to water=3A // RESI TIP3 0=2E000 nodihedral // GROUP =20 // ATOM OH2 OT -0=2E834 // ATOM H1 HT 0=2E417 // ATOM H2 HT 0=2E417 // BOND OH2 H1 OH2 H2 H1 H2 =20 // ANGLE H1 OH2 H2 =20 // ACCEPTOR OH2 =20 // PATCHING FIRS NONE LAST NONE=20 //=20 // I have all the parameters corresponding to water=3A // BONDS // OT HT 450=2E000 0=2E9572=20 // HT HT 0=2E000 1=2E5139=20 // ANGLES // HT OT HT 55=2E000 104=2E5200=20 // NONBONDED // OT 0=2E000000 -0=2E152100 1=2E768200=20 // HT 0=2E000000 -0=2E046000 0=2E224500=20 //=20 // And I have all the topology and parameters of my molecule=2E The output= of // dynamic doesn=27t tell me there is =22MISSING PARAMETER=22 etc=2C it run= s=2E=2E //=20 // I suppose it=27s a problem of interaction between my molecule and water= // molecule but I don=27t know how to introduce it=2E Actualy it=27s the no= n bonded // parameters that manage it=2C and all my atoms are in the list=2E //=20 // I think it=27s not something complicated but I don=27t find the key! // If you have any idea=2C I will read you with pleasure=2E // Thanks a lot=2E //=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=2C please chan= ge // the strange characters on the top line to the =40 sign=2E You can also= // look up the X-Original-From=3A line in the mail header=2E //=20 // E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A // http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage //=20 // E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use // http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage //=20 // Subscribe/Unsubscribe=3A=20 // http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml //=20 // Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet //=20 // Job=3A http=3A//www=2Eccl=2Enet/jobs=20 // Conferences=3A http=3A//server=2Eccl=2Enet/chemistry/announcements/confe= rences/ //=20 // Search Messages=3A http=3A//www=2Eccl=2Enet/chemistry/searchccl/index=2E= shtml //=20 // If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A // http=3A//www=2Eccl=2Enet/spammers=2Etxt //=20 // RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ //=20 //=20 //=20= --- Max-Planck-Institut f=C3=BCr Eisenforschung GmbH Max-Planck-Stra=C3=9Fe 1 D-40237 D=C3=BCsseldorf =20 Handelsregister B 2533=20 Amtsgericht D=C3=BCsseldorf =20 Gesch=C3=A4ftsf=C3=BChrung Prof=2E Dr=2E J=C3=B6rg Neugebauer Prof=2E Dr=2E Dierk Raabe Prof=2E Dr=2E Martin Stratmann Dipl=2E-Kfm=2E Herbert Wilk =20 Ust=2E-Id=2E-Nr=2E=3A DE 11 93 58 514=20 Steuernummer=3A 105 5891 1000 ------------------------------------------------- From owner-chemistry@ccl.net Sun May 10 17:38:00 2009 From: "patris canary patriscanary-*-gmail.com" To: CCL Subject: CCL:G: aromacity Message-Id: <-39268-090510053524-19947-dDy4Gy3Qu10Luiyeg/q9Ng ~ server.ccl.net> X-Original-From: "patris canary" Date: Sun, 10 May 2009 05:35:20 -0400 Sent to CCL by: "patris canary" [patriscanary * gmail.com] Dear All I need the knowledge about calculating aromacity indices like homa, nics, flu pdi and Wiberg bond indices with gaussian 03 keyword or input and output file for this calculation. Thanks in advance Regards... From owner-chemistry@ccl.net Sun May 10 18:13:01 2009 From: "dhacademic dhacademic]~[gmail.com" To: CCL Subject: CCL:G: isotopic NMR calculation in Gaussian Message-Id: <-39269-090509234236-17638-w9w9wAyG2ckNsbf69kEQBQ:+:server.ccl.net> X-Original-From: "dhacademic" Content-Type: multipart/alternative; boundary="=====003_Dragon726860832171_=====" Date: Sat, 9 May 2009 23:42:49 -0500 Mime-Version: 1.0 Sent to CCL by: "dhacademic" [dhacademic*|*gmail.com] This is a multi-part message in MIME format. --=====003_Dragon726860832171_===== Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi, Does anyone know how to do the isotopic NMR calculation in Gaussian? The readisotopes keyword can be used in freq calculation, but no such keyword can be found in the tutorial of NMR. Any suggestion is appreciated. Hao 2009-05-09 dhacademic --=====003_Dragon726860832171_===== Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: 7bit
Hi,
 
Does anyone know how to do the isotopic NMR calculation in Gaussian? The readisotopes keyword can be used in freq calculation, but no such keyword can be found in the tutorial of NMR.
 
Any suggestion is appreciated.
 
Hao
 
2009-05-09
dhacademic
--=====003_Dragon726860832171_=====--