From owner-chemistry@ccl.net Sun May 23 03:34:01 2010 From: "Vigneshwar Ramakrishnan vmsrvignesh|-|gmail.com" To: CCL Subject: CCL:G: Gaussian Error in Internal coordinates Message-Id: <-41922-100523033241-30357-8P6nObCXv/bTxqoOoS+H7g*_*server.ccl.net> X-Original-From: Vigneshwar Ramakrishnan Content-Type: multipart/alternative; boundary=001485f7941c36f2d004873ded6c Date: Sun, 23 May 2010 15:32:29 +0800 MIME-Version: 1.0 Sent to CCL by: Vigneshwar Ramakrishnan [vmsrvignesh..gmail.com] --001485f7941c36f2d004873ded6c Content-Type: text/plain; charset=ISO-8859-1 Dear Ol Ga, Thank you very much for your suggestion. However, strangely, it didn't work out in my case. However, when I gave "Cartesian" keyword, as follows, # ROM062X/3-21G Opt=(Loose,Cartesian) Test The job is running fine (as of now!). Sincerely, Vignesh On Sat, May 22, 2010 at 11:22 PM, Ol Ga eurisco1{}pochta.ru < owner-chemistry|,|ccl.net> wrote: > > Sent to CCL by: "Ol Ga" [eurisco1[]pochta.ru] > Dear Vigneshwar Ramakrishnan, > > I observed this error. It depends on both options - method + basis. If you > choose the level of theory, you should change some positions of atoms - > increase slightly some bond lengths. I made this tune of my "tight" > structure (changed position of 6 atoms from 100 atoms) and new "expanded" > structure converged smoothly without this error. > Anyway, you can optimize your structure on other level and than start the > optimization at the desired level of theory from previously optimized point. > It is an option. > > Sincerely, > > Ol Ga > > -------------------------------------------------- > > From: "Vigneshwar Ramakrishnan vmsrvignesh++gmail.com" > > Sent: Saturday, May 22, 2010 12:34 PM > To: "Ga, Ol " > Subject: CCL:G: Gaussian Error in Internal coordinates > > > > > > > Sent to CCL by: "Vigneshwar Ramakrishnan" [vmsrvignesh##gmail.com] > > Dear All, > > > > I am using (actually, learning!) Gaussian to investigate the properties > of DNA. I generated a 2bp-DNA structure and submitted the *.com file with > ROM062X/3-21G method. However, I get the following error when the job runs. > Could anyone please help me understand the meaning of this error message and > give pointers as to how to fix it? > > > > Cartesian Forces: Max 0.107961092 RMS 0.021734872 > > > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > > Berny optimization. > > NTrRot= -1 NTRed= 730 NAtoms= 126 NSkip= 358 IsLin=F > > Error in internal coordinate system. > > Error termination via Lnk1e in /app1/em64t/g09/l103.exe at Sat May 22 > 16:05:45 2010. > > Job cpu time: 0 days 0 hours 0 minutes 2.9 seconds. > > > > > > Thank you very much, > > Sincerely, > > Vignesh > > > > Graduate Student, > > Dept. of Chem and Biomolecular Engg, > > National University of Singapore. > > Singapore.> > > -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) --001485f7941c36f2d004873ded6c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Ol Ga,
=A0
Thank you very much for your suggestion. However, strangely, it didn&#= 39;t work out in my case. However, when I=A0gave "Cartesian" keyw= ord, as follows,
=A0
# ROM062X/3-21G Opt=3D(Loose,Cartesian) Test
=A0
The job is running fine (as of now!).
=A0
Sincerely,
Vignesh

On Sat, May 22, 2010 at 11:22 PM, Ol Ga eurisco1= {}pochta.ru <owner-chemistry|,|ccl.net> = wrote:

Sent to CCL by: "Ol =A0Ga" [eurisco1[]pochta.ru]
Dear Vig= neshwar Ramakrishnan,

I observed this error. It depends on both opti= ons - method + basis. =A0If you choose the level of theory, you should chan= ge some positions of atoms - increase slightly some bond lengths. I made th= is tune of my "tight" structure (changed position of 6 atoms from= 100 atoms) and new "expanded" structure converged smoothly witho= ut this error.
Anyway, you can optimize your structure on other level and than start the o= ptimization at the desired level of theory from previously optimized point.= It is an option.

Sincerely,

Ol Ga

-------------------= -------------------------------
> From: "Vigneshwar Ramakrishnan vmsrvignesh++gmail.com" <owner-chemistry**ccl.net>
Sent: Saturday, M= ay 22, 2010 12:34 PM
To: "Ga, Ol " <eurisco1**pochta.ru>
Subject: CCL:G: Gaussian Error in Internal= coordinates

>
>
> Sent to CCL by: "Vigneshwar= =A0Ramakrishnan" [vmsrvignesh##gmail.com]
> Dear All,
>
> I am using (ac= tually, learning!) Gaussian to investigate the properties of DNA. I generat= ed a 2bp-DNA structure and submitted the *.com file with ROM062X/3-21G meth= od. However, I get the following error when the job runs. Could anyone plea= se help me understand the meaning of this error message and give pointers a= s to how to fix it?
>
> Cartesian Forces: =A0Max =A0 =A0 0.107961092 RMS =A0 =A0 0.021= 734872
>
> GradGradGradGradGradGradGradGradGradGradGradGradGrad= GradGradGradGradGrad
> Berny optimization.
> NTrRot=3D =A0 =A0-= 1 NTRed=3D =A0 730 NAtoms=3D =A0 126 NSkip=3D =A0 358 IsLin=3DF
> Error in internal coordinate system.
> Error termination via Lnk= 1e in /app1/em64t/g09/l103.exe at Sat May 22 16:05:45 2010.
> Job cpu= time: =A00 days =A00 hours =A00 minutes =A02.9 seconds.
>
>> Thank you very much,
> Sincerely,
> Vignesh
>
> Graduate Student,
> D= ept. of Chem and Biomolecular Engg,
> National University of Singapor= e.
> Singapore.
>
>
>



-=3D This is a= utomatically added to each message by the mailing script =3D-look= up the X-Original-From: line in the mail header.

E-mail to subscrib= ers: CHEMISTRY|,|ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-= mail to administrators: CHEMIS= TRY-REQUEST|,|ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Su= bscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.s= html

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br>
Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
=A0= =A0 =A0http:= //www.ccl.net/spammers.txt

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




--
R.= Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National= University of Singapore,
Singapore

"Strive for Excellence, = Never be satisfied with the second Best!!"

I arise in the morni= ng torn between a desire to improve the world and a desire to enjoy the wor= ld. This makes it hard to plan the day. (E.B. White)
--001485f7941c36f2d004873ded6c-- From owner-chemistry@ccl.net Sun May 23 06:40:01 2010 From: "Dvir Doron dvir.doron!A!gmail.com" To: CCL Subject: CCL: Heat of atomization Message-Id: <-41923-100523041524-23167-Z++kACqIuFv0PqdvZsMcig*_*server.ccl.net> X-Original-From: "Dvir Doron" Date: Sun, 23 May 2010 04:15:22 -0400 Sent to CCL by: "Dvir Doron" [dvir.doron#gmail.com] Hi, how can I calculate heat of atomization so that I can estimate the heat of formation for molecules? A detailed description would be appreciated. What is a practical and accurate approach to computing heats of formation for molecules (directly from ab-initio, dft, or parametric approach)? Thanks, Dvir From owner-chemistry@ccl.net Sun May 23 07:14:00 2010 From: "Tsung-Wen Yen peter308/./gmail.com" To: CCL Subject: CCL: How to generate Symmetry Adapted Basis Function for metallic clusters? Message-Id: <-41924-100523070322-5408-ExrwO94reD1H7Xp5+p4BGg*server.ccl.net> X-Original-From: "Tsung-Wen Yen" Date: Sun, 23 May 2010 07:03:20 -0400 Sent to CCL by: "Tsung-Wen Yen" [peter308:+:gmail.com] Dear CClers: Recently, I calculated Cu38 using DFT software and it has 2ub in magnetism. In order to explain its magnetic properties, I try to use Symmetry Adapted Linear Combination(SALC) method developed by Chemist. But I have encountered some problem. First of all, since the SALC method usually deal with complexies with one center atom, but in my case, Cu38 form a truncated octahedron with Oh symmetry and has six atoms in the center. I wonder if SALC method is applicable to multi-center molecules or clusters? Secondly, I wonder if there are any programs which could output the Symmetry adapted basis function and the Molecular Orbital Diagram after I input the coordinates and elements of the cluster, for example in my case, Cu38? Appreciated for any information which you could provide. With Best Regards Tsung-Wen Yen From owner-chemistry@ccl.net Sun May 23 11:01:00 2010 From: "Brian Salter-Duke brian.james.duke-*-gmail.com" To: CCL Subject: CCL:G: Negative Frequency Message-Id: <-41925-100523040917-7743-rIOMkiC5z4nv1eQeEmh0GQ*_*server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 23 May 2010 09:09:00 +0100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke##gmail.com] This discussion is missing a crucial point. There is a massive difference between DFT methods and Hartree-Fock based methods (including post HF such as MP2 and CCSD). With the latter it is easy to get the magnitude of the smallest frequency to be less than 2 cm-1. If it is not, just reoptimize with a tighter condition. However, DFT in Gaussian uses a grid and that makes the result not rotationally invariant. The energy will change slightly if you rotate the molecule in the coordinate system (you will usually not notice this because the progran will always change your coordinates to the standard orientation). Another consequence is that the magnitude of the smallest frequency is not zero. This will be particularly bad if there is a heavy element in your molecule. For Ga - Br values of the magnitude of the smallest frequency in the range 40 - 70 cm-1 are common. Using a tighter grid can help, but not that much. When you report this problem here, please report all the lowest 8 or so frequencies, including the 3 translational ones, which should be very small, and the three rotational ones, which with DFT can also be well off zero. The bottom line for DFT is that the lowest frequency can often be ignored, but only with care. Brian. On Sat, May 22, 2010 at 05:20:52PM +0000, Cristina Aparecida Barboza crissetubal(!)gmail.com wrote: > Dear William Flak, > > I heard the same before, that small negative frequencies can be ignored, but > I think that -50 or -19 cm-1 are too high to be neglected. A small frequency > would be less than 2 cm-1. You should try to do a preoptimization with a > semiempirical method as PM6 in Gaussian or Mopac then to do your > optimization with B3LYP/6-311++G** or B3LYP/6-31G*. > > Best regards > > -- > M.Sc. Cristina Aparecida Barboza > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Doctorado en Fisicoquímica Molecular, > Facultad de Ecología y Recursos Naturales, > Universidad Andrés Bello - UNAB, > Santiago, Chile > > Laboratorio de Quimica Teorica, > Facultad de Quimica y Biologia, > Universidad de Santiago de Chile - USACH, > Santiago, Chile -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: b_duke(0)bigbond.net.au Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Sun May 23 11:36:00 2010 From: "nazanin jamshidi na.jamshidi---gmail.com" To: CCL Subject: CCL:G: Optional value for the dielectric constant Message-Id: <-41926-100523094708-18408-763Fwc+5a3NIk5Ahf+FWzQ++server.ccl.net> X-Original-From: nazanin jamshidi Content-Type: multipart/alternative; boundary=0016e6469708a7523d0487432867 Date: Sun, 23 May 2010 06:47:01 -0700 MIME-Version: 1.0 Sent to CCL by: nazanin jamshidi [na.jamshidi._._.gmail.com] --0016e6469708a7523d0487432867 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear all I try to use "EPSINF=3Dval" keyword in G03 but I do not know where can I fi= nd the value for different solvents. This is a list of the solvents I need numerical value of the dynamic (or optical) dielectric constant of them. =EF=BB=BFCyclohexane Hexane (n-Hexane) Heptane Triethylamine Tetrachloromethane Toluene Thank you so much N.Jamshidi --0016e6469708a7523d0487432867 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear all
=C2=A0
I try=C2=A0to use "EPSINF=3Dval"=C2=A0keyword in G03 but I d= o not know=C2=A0where can I find the value for different solvents.=C2=A0=C2= =A0=C2=A0=C2=A0
=C2=A0
This is a list of the solvents I need numerical value of the dynamic (= or optical) dielectric constant of them.
=EF=BB=BFCyclohexane
Hexane (n-Hexane)
Heptane
Triethylamin= e
Tetrachloromethane
Toluene
=C2=A0
Thank you so much
=C2=A0
N.Jamshidi
=C2=A0

--0016e6469708a7523d0487432867-- From owner-chemistry@ccl.net Sun May 23 12:11:00 2010 From: "nazanin jamshidi na.jamshidi:gmail.com" To: CCL Subject: CCL:G: Optional value for the dielectric constant Message-Id: <-41927-100523023444-13498-rrywwblmWNfTIHntHQ+4RQ===server.ccl.net> X-Original-From: nazanin jamshidi Content-Type: multipart/alternative; boundary=0016e65c7ca0460dda04873d1e07 Date: Sun, 23 May 2010 11:04:37 +0430 MIME-Version: 1.0 Sent to CCL by: nazanin jamshidi [na.jamshidi]~[gmail.com] --0016e65c7ca0460dda04873d1e07 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear all I try to use "EPSINF=3Dval" keyword in gaussian 03 but I do not know where = can I find the value for different solvents. This is a list of the solvents I need numerical value of the dynamic (or optical) dielectric constant of them. =EF=BB=BFCyclohexane Hexane (n-Hexane) Heptane Triethylamine Tetrachloromethane Toluene Thank you so much N.Jamshidi --0016e65c7ca0460dda04873d1e07 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear all
=C2=A0
I try=C2=A0to use "EPSINF=3Dval"=C2=A0keyword in gaussian 03= but I do not know=C2=A0where can I find the value for different solvents.= =C2=A0=C2=A0=C2=A0=C2=A0
=C2=A0
This is a list of the solvents I need numerical value of the dynamic (= or optical) dielectric constant of them.
=EF=BB=BFCyclohexane
Hexane (n-Hexane)
Heptane
Triethylamin= e
Tetrachloromethane
Toluene
=C2=A0
Thank you so much
=C2=A0
N.Jamshidi
=C2=A0
--0016e65c7ca0460dda04873d1e07-- From owner-chemistry@ccl.net Sun May 23 12:46:00 2010 From: "Parikshit Moitra prkshtmoitra-*-gmail.com" To: CCL Subject: CCL: problem installing tinker modelling package in ubuntu Message-Id: <-41928-100523093006-9621-GxAs7yNsYw0YFX3BvRkP1g~~server.ccl.net> X-Original-From: "Parikshit Moitra" Date: Sun, 23 May 2010 09:30:05 -0400 Sent to CCL by: "Parikshit Moitra" [prkshtmoitra#gmail.com] Hello, I am very new to this and I am unable to install tinker modelling package in ubuntu 9.10 system. Can anyone help me in this regard? I will be grateful to you. From owner-chemistry@ccl.net Sun May 23 15:11:00 2010 From: "Sayan Mondal sayanmondal.ncbs^^gmail.com" To: CCL Subject: CCL: Free Energy of Solvation Message-Id: <-41929-100523122944-20406-5tBYLYcZd0BnUHkvkyUIfg=-=server.ccl.net> X-Original-From: Sayan Mondal Content-Type: multipart/alternative; boundary=00504502ce8a0449f90487456e76 Date: Sun, 23 May 2010 21:59:35 +0530 MIME-Version: 1.0 Sent to CCL by: Sayan Mondal [sayanmondal.ncbs|*|gmail.com] --00504502ce8a0449f90487456e76 Content-Type: text/plain; charset=ISO-8859-1 Hi, Can any one tell me the procedure of computing free energy of solvation of any molecule using ab initio methods. Please tell which energies to calculate and which one has to be subtracted from what ? Can comparison of free energy of solvation be used to comment on tautomeric equilibrium of any molecule (organic) ? thanks sayan --00504502ce8a0449f90487456e76 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
Can any one tell me the procedure of computing free energy of solvat= ion of any molecule using ab initio methods. Please tell which energies to = calculate and which one has to be subtracted from what ?

Can compar= ison of free energy of solvation be used to comment on tautomeric equilibri= um of any molecule (organic) ?


thanks
sayan=A0


--00504502ce8a0449f90487456e76-- From owner-chemistry@ccl.net Sun May 23 17:05:00 2010 From: "Jim Kress ccl_nospam~~kressworks.com" To: CCL Subject: CCL:G: Optional value for the dielectric constant Message-Id: <-41930-100523153028-25739-VQuVDNvbAkjrLb6/gfNpGA ~~ server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01CAFA8C.D4329290" Date: Sun, 23 May 2010 15:30:07 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%a%kressworks.com] This is a multi-part message in MIME format. ------=_NextPart_000_0004_01CAFA8C.D4329290 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Google is your friend: =20 http://clippercontrols.com/pages/dielectric-values =20 Jim =20 > From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com~~ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com~~ccl.net] On = Behalf Of nazanin jamshidi na.jamshidi:gmail.com Sent: Sunday, May 23, 2010 2:35 AM To: Kress, Jim Subject: CCL:G: Optional value for the dielectric constant =20 Dear all =20 I try to use "EPSINF=3Dval" keyword in gaussian 03 but I do not know = where can I find the value for different solvents. =20 =20 This is a list of the solvents I need numerical value of the dynamic (or = optical) dielectric constant of them. =EF=BB=BFCyclohexane=20 Hexane (n-Hexane) Heptane=20 Triethylamine=20 Tetrachloromethane=20 Toluene=20 =20 Thank you so much =20 N.Jamshidi =20 ------=_NextPart_000_0004_01CAFA8C.D4329290 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Google is your friend:

 

http://clippe= rcontrols.com/pages/dielectric-values

 

Jim

 

From:= owner-chemistry+ccl_nospam=3D=3Dkressworks.com~~ccl.net [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com~~ccl.net] On = Behalf Of nazanin jamshidi na.jamshidi:gmail.com
Sent: Sunday, May 23, 2010 2:35 AM
To: Kress, Jim
Subject: CCL:G: Optional value for the dielectric = constant

 

Dear all

 

I try to use = "EPSINF=3Dval" keyword in gaussian 03 but I do not know where can I find the value for = different solvents.    

 

This is a list of the solvents I need numerical = value of the dynamic (or optical) dielectric constant of them.

=EF=BB=BFCyclohexane
Hexane (n-Hexane)
Heptane
Triethylamine
Tetrachloromethane
Toluene

 

Thank you so much

 

N.Jamshidi

 

------=_NextPart_000_0004_01CAFA8C.D4329290-- From owner-chemistry@ccl.net Sun May 23 17:40:01 2010 From: "Jim Kress ccl_nospam!A!kressworks.com" To: CCL Subject: CCL: Optional value for the dielectric constant Message-Id: <-41931-100523153415-11199-3Nj2zZwvCfCCfgRczsR8PQ . server.ccl.net> X-Original-From: "Jim Kress" Date: Sun, 23 May 2010 15:34:14 -0400 Sent to CCL by: "Jim Kress" [ccl_nospam++kressworks.com] Google is your friend: http://clippercontrols.com/pages/dielectric-values Jim From owner-chemistry@ccl.net Sun May 23 18:25:00 2010 From: "David Hose anthrax_brothers|,|hotmail.com" To: CCL Subject: CCL:G: Optional value for the dielectric constant Message-Id: <-41932-100523182258-12766-tcVvgveEkyQWMrPBBYS+vQ::server.ccl.net> X-Original-From: "David Hose" Date: Sun, 23 May 2010 18:22:56 -0400 Sent to CCL by: "David Hose" [anthrax_brothers~~hotmail.com] Jamshidi, Firstly, four of the solvents you list are built into G03. G09, if you have access has a hugely expanded list of solvents (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm). Secondly, this type of question has come up on the list before. You might find my post from March 2008 helpful as it not only covers the EPSINF question (Thanks to Marcel Swart's advice about calculating the value from the refractive index), but also some information regarding the RSolv value. http://www.ccl.net/cgi-bin/ccl/message-new?2008+03+11+010 Hope this helps. Regards, Dave. ============ CCL:G: Optional value for the dielectric constant > From: nazanin jamshidi Subject: CCL:G: Optional value for the dielectric constant Date: Sun, 23 May 2010 06:47:01 -0700 Dear all I try to use "EPSINF=val" keyword in G03 but I do not know where can I find the value for different solvents. This is a list of the solvents I need numerical value of the dynamic (or optical) dielectric constant of them. Cyclohexane Hexane (n-Hexane) Heptane Triethylamine Tetrachloromethane Toluene Thank you so much N.Jamshidi From owner-chemistry@ccl.net Sun May 23 23:38:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim+/-compchem.net" To: CCL Subject: CCL: ionic bond and the charges of its corresponding atoms Message-Id: <-41933-100523171003-16227-f4LV2Dbs3gGyu38QZflnmg::server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016364c7eaf6086170487495812 Date: Sun, 23 May 2010 22:09:51 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim .. compchem.net] --0016364c7eaf6086170487495812 Content-Type: text/plain; charset=ISO-8859-1 Dear May Ionic bond is a bond formed between oppositely charged ions, so in your case, your bond is not ionic and couldn't call it ionic because its corresponding atoms bear the same charge. In your system, this bonding type is called repulsion interaction, an interaction occurred between atoms bearing the same charge. It has been studied extensively in the last decade. but, it is still open area for further studies. If you are sure your bond type is ionic, so the problem may be returned to your method for charge calculation. By the way, regarding to your previous enquiry, you haven't posted more information about your system. But, it is correct as another researcher kindly added, sulfate ions occasionally come from buffer solution, and as he also kindly mentioned it is sometimes *neccessary* to remove it, but it is * sometimes*. We remove sulfate ions coming from buffer system when we are sure they/it have/has no effect on the binding affinity of the studied inhibitor(s) and no effect on the active site geometry. But in your case, sulfate ions are close to the active site, and you are doing docking study; replacing sulfate ions with other molecule(s) (neutral or charged) or removing them is considered as a blind trick. You should study your system modifications in case you replaced or removed sulfate ions by MM study, before going on further in your research, and see how your system has been changed by your modifications. Sincerely; M. Ibrahim On Fri, May 21, 2010 at 8:33 PM, may abdelghani may01dz-,-yahoo.fr < owner-chemistry!^!ccl.net> wrote: > fear CCLesr, > > A bond X-Y has a degree of ionic character, or it is an ionic bond. But its > corresponding atoms have the same charge type (both negative for > example)????????? its a normal case > > > > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim!^!compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016364c7eaf6086170487495812 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear May
Ionic bond is a bond formed between=A0oppositely=A0charged ion= s, so in your case, your bond is not ionic and couldn't call it=A0ionic= =A0because its corresponding atoms bear the same charge.
In your = system, this bonding type is called repulsion interaction, an interaction= =A0occurred=A0between atoms bearing the same charge. It has been studied ex= tensively in the last decade. but, it is still open area for=A0further=A0st= udies.
If you are sure your bond type is ionic, so the problem may be returne= d to your method for charge calculation.

By the wa= y, regarding to your previous enquiry, you haven't posted more informat= ion about your system. But, it is correct as another researcher kindly adde= d, sulfate ions=A0occasionally=A0come from=A0buffer=A0solution, and as he a= lso kindly mentioned it is=A0sometimes=A0neccessary to remove it, bu= t it is sometimes.
We remove sulfate ions coming from buffer system when we are sure they= /it have/has no effect on the binding affinity of the studied inhibitor(s) = and no effect on the active site geometry. But in your case, sulfate ions a= re close to the active site, and you are doing docking study; replacing sul= fate ions with other molecule(s) (neutral or charged) or removing them is c= onsidered as a blind trick. You should study your system modifications in c= ase you replaced or removed sulfate ions by MM study, before going on furth= er in your research, and see how your system has been changed by your modif= ications.

Sincerely;
M. Ibrahim



On Fri, May 21, 2010 at 8:33 PM, may a= bdelghani may01dz-,-yahoo.fr <owner-chemistry!^!ccl.net<= /a>> wrote:
fear CCLe= sr,

A bond X-Y has a de= gree of ionic character, or it is an ionic bond. But its corresponding atom= s have the same charge type (both negative for example)????????? its a norm= al case



=




--
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Univ= ersity of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim!^!compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--0016364c7eaf6086170487495812--