From owner-chemistry@ccl.net Sat Feb 21 01:08:01 2009 From: "Reaz Uddin riaasuddin=yahoo.com" To: CCL Subject: CCL: azide atom types Message-Id: <-38695-090220062821-30373-OBnt2Fw7uvPLE7KS5Zua5Q ~~ server.ccl.net> X-Original-From: Reaz Uddin Content-Type: multipart/alternative; boundary="0-1094736776-1235129286=:3596" Date: Fri, 20 Feb 2009 03:28:06 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin()yahoo.com] --0-1094736776-1235129286=:3596 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Thank you so much all. It helps to understand. REAZUDDIN=20 Research Scholar=20 HEJ Research Institute of Chemistry University of Karachi Karachi, Pakistan Email: riaasuddin---yahoo.com, mriazuddin---iccs.edu --- On Thu, 2/19/09, Bob Clark bclark###bcmetrics.com wrote: > From: Bob Clark bclark###bcmetrics.com Subject: CCL: azide atom types To: "UDDIN, REAZ " Date: Thursday, February 19, 2009, 10:19 PM Hi Reaz, The atom typing that Wayne suggests is probably the best that you are going= to find. Bear in mind, however, that azide is close kin to ozone, and is actua= lly slightly bent (5-10 degrees away from the N1 substituent) for the same reas= ons. Hence the linear geometry imposed by a central N.1 atom type will be a litt= le off if you try to optimize it - even if you use the Merck force field. See, e.g., Klaboe et al. J Mol Str 1987, 160, 245-257 (http://folk.uio.no/clausn/papers_81-90/J_Mol_Struct_1987_160_245-257.pdf) Good luck, Bob C. > Wayne Steinmetz WES04747:_:pomona.edu wrote: >>=20 >> SYBYL=E2=80=99s sketch module allows one to construct a molecule using substituents and fortunately the azide group is on the list. >>=20 >> Here is the atom typing in brackets for each heavy atom in methylazide (H_3 CNNN): C[C3]N[N2]N[N1]N[N2] . >>=20 >> Wayne E. Steinmetz >> Professor Emeritus of Chemistry >> USFS Volunteer >> Chemistry Department >> Pomona College >> 645 North College Avenue >> Claremont, California 91711-6338 >> USA >> phone: 1-909-621-8447 >> FAX: 1-909-607-7726 >> Email: wsteinmetz,+,pomona.edu >> WWW: pages.pomona.edu/~wsteinmetz >>=20 >> ------------------------------------------------------------------------ >>=20 >> *From:* owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu,+,ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu,+,ccl.net] *On= Behalf Of *Reaz Uddin riaasuddin^-^yahoo.com >> *Sent:* Tuesday, February 17, 2009 11:01 PM >> *To:* Wayne Steinmetz >> *Subject:* CCL: atom types >>=20 >> Hi Folks, >>=20 >> I was just wondering what should be the atom types of each Nitrogen in Azide group (**R****-N=3DN^+ =3DN^- ** ) in Sybyl or any common molecular o= perating programs ?? >>=20 >> Thank you so much for your time. >>=20 >> REAZUDDIN >> Research Scholar >> HEJ Research Institute of Chemistry >> University of Karachi >> Karachi, Pakistan >> Email: riaasuddin=3Dyahoo.com, mriazuddin=3Diccs.edu >>=20 >> ------------------------------------------------------------- >> This message has been scanned by Postini anti-virus software. >>=20 >> =0A=0A=0A --0-1094736776-1235129286=:3596 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Thank you so much = all. It helps to understand.

REAZUDDIN
Research Scholar <= /SPAN>
HEJ Research Institute of Chemistry
University of Karachi
Karachi, Pakistan
Email: riaasuddin---yahoo.com, mriazuddin---iccs.edu


--- On = Thu, 2/19/09, Bob Clark bclark###bcmetrics.com <owner-chemistry---ccl.n= et> wrote:
From: Bob Clark bclark###bcmetrics.com <owner-chem= istry---ccl.net>
Subject: CCL: azide atom types
To: "UDDIN, REAZ -id= #3zj-" <riaasuddin---yahoo.com>
Date: Thursday, February 19, 2009, 1= 0:19 PM

Hi Reaz,

The atom typing that Wayne suggests is probably the best that you are going=
 to
find. Bear in mind, however, that azide is close kin to ozone, and is actua=
lly
slightly bent (5-10 degrees away from the N1 substituent) for the same reas=
ons.
Hence the linear geometry imposed by a central N.1 atom type will be a litt=
le
off if you try to optimize it - even if you use the Merck force field.

See, e.g., Klaboe et al. J Mol Str 1987, 160, 245-257
(http://folk.uio.no/clausn/papers_81-90/J_Mol_Struct_1987_160_245-257.pdf)

Good luck,

Bob C.
> Wayne Steinmetz WES04747:_:pomona.edu wrote:
>>=20
>> SYBYL=E2=80=99s sketch module allows one to construct a molecule u=
sing
substituents and fortunately the azide group is on the list.
>>=20
>> Here is the atom typing in brackets for each heavy atom in methyla=
zide
(H_3 CNNN): C[C3]N[N2]N[N1]N[N2] .
>>=20
>> Wayne E. Steinmetz
>> Professor Emeritus of Chemistry
>> USFS Volunteer
>> Chemistry Department
>> Pomona College
>> 645 North College Avenue
>> Claremont, California 91711-6338
>> USA
>> phone: 1-909-621-8447
>> FAX: 1-909-607-7726
>> Email: wsteinmetz,+,pomona.edu
>> WWW: pages.pomona.edu/~wsteinmetz
>>=20
>>
------------------------------------------------------------------------
>>=20
>> *From:* owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu,+,ccl=
.net
[mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu,+,ccl.net] *On=
 Behalf
Of *Reaz Uddin riaasuddin^-^yahoo.com
>> *Sent:* Tuesday, February 17, 2009 11:01 PM
>> *To:* Wayne Steinmetz
>> *Subject:* CCL: atom types
>>=20
>> Hi Folks,
>>=20
>> I was just wondering what should be the atom types of each Nitroge=
n in
Azide group (**R****-N=3DN^+ =3DN^- ** ) in Sybyl or any common molecular o=
perating
programs ??
>>=20
>> Thank you so much for your time.
>>=20
>> REAZUDDIN
>> Research Scholar
>> HEJ Research Institute of Chemistry
>> University of Karachi
>> Karachi, Pakistan
>> Email: riaasuddin=3Dyahoo.com, mriazuddin=3Diccs.edu
<mailto:mriazuddin=3Diccs.edu>
>>=20
>> -------------------------------------------------------------
>> This message has been scanned by Postini anti-virus software.
>>=20
>>

=0A=0A=0A=0A --0-1094736776-1235129286=:3596-- From owner-chemistry@ccl.net Sat Feb 21 04:24:00 2009 From: "Tomasz Grabarkiewicz grabar * man.poznan.pl" To: CCL Subject: CCL: calculate plane b/w 2 tryptophans Message-Id: <-38696-090221041843-16905-Mg8pfjGiQCzjNpv+Rkdt/g[#]server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Sat, 21 Feb 2009 09:36:04 +0100 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar . man.poznan.pl] Anjan, Mercury, which is free, has a built-in option to calculate the dihedral angle between user defined planes. Take a look at: http://www.ccdc.cam.ac.uk/products/mercury/ Tomasz From owner-chemistry@ccl.net Sat Feb 21 22:38:00 2009 From: "Chaofu Wu xiaowu759||hotmail.com" To: CCL Subject: CCL: Can the structure built by Amorphous Cell of Materials Studio be used? Message-Id: <-38697-090220194447-9814-GIjxcwZcuzXcnh929bvV5g||server.ccl.net> X-Original-From: "Chaofu Wu" Date: Fri, 20 Feb 2009 19:44:43 -0500 Sent to CCL by: "Chaofu Wu" [xiaowu759**hotmail.com] Hi, everybody, I am a freshman for using GROMACS. I used to do simulations using Materials Studio. Now I notice that versatile analysis tools are present in GROMACS, so I decide to turn for GROMACS. I have built some polymeric structures using the Amorphous Cell module in Materials Studio4.0. Can these structures be directly input into GROMACS for a further simulations? How can I do that? Can you give some hints? Is there any software or tools available? Thanks a lot in advance. Xiaowu From owner-chemistry@ccl.net Sat Feb 21 23:13:00 2009 From: "Alex Liu ylvn8_-_umkc.edu" To: CCL Subject: CCL: Any molecular mechanics model good at pi-pi stacking calculation? Message-Id: <-38698-090221021937-10551-NWo+A2ARhyirWOxTdCANSg#server.ccl.net> X-Original-From: "Alex Liu" Date: Sat, 21 Feb 2009 02:19:33 -0500 Sent to CCL by: "Alex Liu" [ylvn8,,umkc.edu] The molecules I am working on have over 200 atoms. I am wondering is there any MM or semiempirical package that is able to handle pi-pi stacking engeries relatively accurately? Alex ylvn8##umkc.edu From owner-chemistry@ccl.net Sat Feb 21 23:49:01 2009 From: "John McKelvey jmmckel() gmail.com" To: CCL Subject: CCL:G: oxygen charge varies using b3lyp/631g* and aug-cc-pvdz in gaussian 03 Message-Id: <-38699-090220104323-14672-1b0gFmq+9LKAduNV6os+8g]*[server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=000e0cd14efc856a4d04635b8296 Date: Fri, 20 Feb 2009 10:43:09 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel---gmail.com] --000e0cd14efc856a4d04635b8296 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit With respect to Jens' comment I have a related question, and a completely non-related one. I think that if one has the core orbitals on an atom "saturated" then basis set superposition errors due to that atom's using neighboring orbitals, such as more diffuse neighboring d fns, tend to be minimized. If this is true, what would be the effect in a molecular environment if one added more orbitals to an already saturated isolated-atom basis set? Completely off the question: Has anyone run any MO program, semi-empirical or otherwise, using a VMPlayer linux appliance? How bad a hit in performance against running it native might be observed? Many thanks! John McKelvey On Thu, Feb 19, 2009 at 10:22 AM, Jens Spanget-Larsen spanget-x-ruc.dk < owner-chemistry|-|ccl.net> wrote: > > Sent to CCL by: Jens Spanget-Larsen [spanget[-]ruc.dk] > > Dear Sohail, > the results of a Mulliken population analysis with a basis set like > aug-cc-pvdz that includes diffuse functions are essentially meaningless. In > a Mulliken analysis, population due to the diffuse functions is counted as a > contribution to the center where the functions are defined, but these > functions tend to have large amplitude on the neighbouring centers! - You > should perform, e.g., a "natural population analysis", or one of the > analyses based on the fitting of electrostatic potentials and so forth. > There are several possibilities, that are much less basis set dependent. > Yours, Jens >--< > > ------------------------------------------------------ > JENS SPANGET-LARSEN Office: +45 4674 2710 > Dept. of Science (18.1) Fax: +45 4674 3011 > Roskilde University Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget]|[ruc.dk > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > ------------------------------------------------------ > > > > sohail sohail meandme_meandme2003[-]yahoo.com wrote: > >> Sent to CCL by: "sohail sohail" [meandme_meandme2003[]yahoo.com] >> hi, i have done optimization of dodecahedron water clusters using gaussian >> 03 program. My question is that mulliken charges on oxygen atoms are around >> -1.2 using b3lyp/631g* while xygen charge is -0.3 using b3lyp/aug-cc-pvdz. >> can u pls tell me why this so much charge difference by using 2 different >> basis sets on the same level of theory. how should i put the results in >> paper if there is this much variation in results. thanks. >> sohail.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --000e0cd14efc856a4d04635b8296 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable With respect to Jens' comment I have a related question, and a complete= ly non-related one.

I think that if one has the core orbitals on an = atom "saturated" then basis set superposition errors due to that = atom's using neighboring orbitals, such as more diffuse neighboring d f= ns, tend to be minimized.  If this is true, what would be the effect i= n a molecular environment if one added more orbitals to an already saturate= d isolated-atom basis set?

Completely off the question:  Has anyone run any MO program, semi-= empirical or otherwise, using a VMPlayer linux appliance?  How bad a h= it in performance against running it native might be observed?

Many = thanks!

John McKelvey 

On Thu, Feb 19, = 2009 at 10:22 AM, Jens Spanget-Larsen s= panget-x-ruc.dk <owner-chemistry|-|ccl.net> wrote:

Sent to CCL by: Jens Spanget-Larsen [spanget[-]ruc.dk]

Dear Sohail,
the results of a Mulliken population analysis with a basis set like aug-cc-= pvdz that includes diffuse functions are essentially meaningless. In a Mull= iken analysis, population due to the diffuse functions is counted as a cont= ribution to the center where the functions are defined, but these functions= tend to have large amplitude on the neighbouring centers! - You should per= form, e.g., a "natural population analysis", or one of the analys= es based on the fitting of electrostatic potentials and so forth. There are= several possibilities, that are much less basis set dependent.
Yours, Jens >--<

 ------------------------------------------------------
 JENS SPANGET-LARSEN         Office:    =  +45 4674 2710
 Dept. of Science (18.1)     Fax:        = ; +45 4674 3011
 Roskilde University         Mobile:    =  +45 2320 6246
 P.O.Box 260                 E= -Mail:     spanget]|[= ruc.dk
 DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
 ------------------------------------------------------



sohail sohail meandme_meandme2003[-]yahoo.com wrote:
Sent to CCL by: "sohail  sohail" [meandme_meandme2003[]yahoo.com]
hi, i have done optimization of dodecahedron water clusters using gaussian = 03 program. My question is that mulliken charges on oxygen atoms are around= -1.2 using b3lyp/631g* while xygen charge is -0.3 using b3lyp/aug-cc-pvdz.= can u pls tell me why this so much charge difference by using 2 different = basis sets on the same level of theory. how should i put the results in pap= er if there is this much variation in results. thanks.
sohail.>





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