From owner-chemistry@ccl.net Sun May 4 02:06:01 2008 From: "Cheng, Tiejun tjcheng|mail.sioc.ac.cn" To: CCL Subject: CCL: rmsd problem Message-Id: <-36885-080503230203-27929-d3jRwebDKMPwr3DYJMgDWQ()server.ccl.net> X-Original-From: "Cheng, Tiejun" Content-Type: multipart/alternative; boundary="----=_Part_2546_25673685.1209870106625" Date: Sun, 4 May 2008 11:01:46 +0800 MIME-Version: 1.0 Sent to CCL by: "Cheng, Tiejun" [tjcheng[A]mail.sioc.ac.cn] ------=_Part_2546_25673685.1209870106625 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, Sobia In GOLD, you can use $GOLD_DIR/utilities/smart_rms to calculate RMSD between two molecules. Jay On 5/3/08, Reaz Uddin riaasuddin[#]yahoo.com wrote: > > Sent to CCL by: Reaz Uddin [riaasuddin*o*yahoo.com] > > RMSD.svl in MOE is for calculating rmsds for different conformations of same ligand. It is not for the different ligand. > GOLD provides an RMSD matrix at the end of log file and you can easily figure out RMSDs between different pairs of conformations/solutions of the same ligand. > > > > REAZUDDIN > Research Scholar > Department of Medicinal Chemistry and Pharmacognosy, > College of Pharmacy, (M/C 781) > University of Illinois at Chicago > 833 S. Wood St. > Chicago, IL 60612 > > > --- On *Wed, 4/30/08, sobia ahsan halim sobia_halim[a]yahoo.com > * wrote: > > From: sobia ahsan halim sobia_halim[a]yahoo.com > > Subject: CCL: rmsd problem > To: "UDDIN, REAZ " > Date: Wednesday, April 30, 2008, 3:49 PM > > Sent to CCL by: "sobia ahsan halim" [sobia_halim-x-yahoo.com] > hello all > > I am facing problem regarding rmsd. I am calculating the rmsd through MOE > but when I use structurally different > compound to measure rmsd against the > reference molecule (co-crystallized with the protein), it doesn't show any > rmsd value and give the error that the molecule is structurally not similar. > And the other thing is how to calculate rmsd on GOLD as GOLD log file > contain rmsd value but it is the rmsd of the cluster not of different > conformations of docked ligand. Can any one please tell me how to solve both > these problems???. Thanks in advance. > > With the deepest regards, > Sobia. > > > > ------------------------------ > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it > now. recover the email address of the author of the message, please change the > strange characters on the top line to the |-| sign. You can also look up the > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY|-|ccl.net or use:E-mail to administrators: > CHEMISTRY-REQUEST|-|ccl.net or useBefore posting, check wait > time at: http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/htdig (login: ccl, Password: search) If your > mail bounces from CCL with 5.7.1 error, check:RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ ------=_Part_2546_25673685.1209870106625 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi, Sobia
 
In GOLD, you can use $GOLD_DIR/utilities/smart_rms to calculate RMSD b= etween two molecules.
 
Jay
 


On 5/3/08, R= eaz Uddin riaasuddin[#]yahoo.com <<= a href=3D"mailto:owner-chemistry|-|ccl.net">owner-chemistry|-|ccl.net> w= rote:
Sent to CCL by: Reaz Uddin [riaa= suddin*o*yahoo.com]=20 
RMSD.svl in MOE is for calculating r=
msds for different conformations of same ligand. It is not for the differen=
t ligand. 
GOLD provides an RMSD matrix at the end of log file and you c=
an easily figure out RMSDs between different pairs of conformations/solutio=
ns of the same ligand.


REAZUDDIN
Research Scho= lar
Department of Medicinal Chemistry and Pharmacognosy,
College of Pharmacy, (M/C 781) <= br style=3D"COLOR: rgb(0,0,127)">Univer= sity of Illinois at Chicago
833 S. Wood St.
Chicago, IL 60612
=

--- On Wed, 4/30/08, sobia ahsan halim sobia_halim[a]yahoo.com <owner-chemistry|,|ccl.net> wrote:
From: sobia ahsan halim sobia_halim[a]yahoo.com <owner-chemistry|,|ccl.net>
Subject: CCL: rmsd problem
To: "UDDIN, REAZ " <riaasuddin|,= |yahoo.com>
Date: Wednesday, April = 30, 2008, 3:49 PM

Sent to CCL by: "sobia ahsan halim" [sobia_halim-x-yahoo.com]
hello all

I=
 am facing problem regarding rmsd. I am calculating the rmsd through MOE 
but when I use structurally different
 compound to measure rmsd against the 
reference molecule (co-crystalliz=
ed with the protein), it doesn't show any 
rmsd value and give the e=
rror that the molecule is structurally not similar. 
And the other thing=
 is how to calculate rmsd on GOLD as GOLD log file 

contain rmsd value but it is the rmsd of the cluster not of different 
c=
onformations of docked ligand. Can any one please tell me how to solve both=
 
these problems???. Thanks in advance.

With the deepest regards,=


Sobia.



Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -=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 the strange characters on the top = line to the |-| sign. You can also look up the X-Original-From: line in the m= ail header. E-mail to subscribers: CHE= MISTRY|-|ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to a= dministrators: CHEMISTRY-REQUE= ST|-|ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubs= cribe: http://www.= ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: <= a onclick=3D"return top.js.OpenExtLink(window,event,this)" href=3D"http://w= ww.ccl.net/" target=3D"_blank">http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.= net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/htdig (login: ccl, Password:= search)http://www.ccl.net/spammers.txt RTFI:= http://www= .ccl.net/chemistry/aboutccl/instructions/

------=_Part_2546_25673685.1209870106625-- From owner-chemistry@ccl.net Sun May 4 04:41:01 2008 From: "Mike Ramos mikeart9+/-yahoo.com" To: CCL Subject: CCL:G: OPT+Freq calculation Message-Id: <-36886-080503013552-2484-4GL2XjaGBWuL3N92sQYL4g*|*server.ccl.net> X-Original-From: "Mike Ramos" Date: Sat, 3 May 2008 01:35:49 -0400 Sent to CCL by: "Mike Ramos" [mikeart9]^[yahoo.com] Hi all, I have a question regarding the OPT+Freq calculation on a organic dye molecule containing aromatic ring, N and S. when I perform a combine OPT+Freq calculations using g98 suite I get the following output, however, the job is terminated normally. A part of the output is, Exact polarizability: 460.270 0.017 165.147 -0.011 0.004 83.671 Approx polarizability: 946.252 0.009 298.846 -0.071 -0.001 135.419 Full mass-weighted force constant matrix: Low frequencies --- -13.1622 -9.1671 -0.4072 -0.0102 0.0113 0.0301 Low frequencies --- 46.4240 76.1170 160.3242 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 46.3783 76.1118 160.3242 Red. masses -- 6.8205 4.0843 4.7897 Frc consts -- 0.0086 0.0139 0.0725 IR Inten -- 6.5969 0.0000 0.0039 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 The input contains the following command, # opt freq b3lyp/6-311+g(d) scf=(qc,maxcycle=500,conver=5) geom=connectivity gfinput iop(6/7=3) My question is why do I get "?" mark in the output file. Am I making any mistak? Thanks in advance mike From owner-chemistry@ccl.net Sun May 4 05:21:01 2008 From: "Barbara Murray barbara_murray~!~redlands.edu" To: CCL Subject: CCL:G: Undergraduate research question Message-Id: <-36887-080504010752-4952-9ByEhgSJzx+m+je1QgFFbQ() server.ccl.net> X-Original-From: Barbara Murray Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 03 May 2008 22:09:36 -0700 MIME-Version: 1.0 Sent to CCL by: Barbara Murray [barbara_murray]=[redlands.edu] Let me give the list some background before I try to ask my question. I teach organic chemistry at a small private, undergraduate university. I was trained as a solid state synthetic chemist about 30 years ago. About 15 years ago I became interested in computational chemistry and have dabbled in it ever since. I say dabbled because a) although faculty are encouraged to stay professionally active here, teaching is our first priority (and my first love) and b) for the last 10 years I've been a half time administrator so I have little time to do research. All of our chemistry majors do at least a senior research project and some do much more. I've had the occasional student work for me doing what I call computational studies of biologically active molecules. A student does a literature search to find a set of biologically interesting molecules that all work on the same receptor (one example was protease inhibitors when they were first coming out). The student then uses computational chemistry (usually electrostatic potentials) and information about the receptor's active site to determine why one molecule might work better than another. These are not earth shaking projects (nor publishable), but the students learn a bit about computational chemistry and I'm generally happy. But my problem (or not) is that I now have one of the smartest students I've had in over 20 years who wants to work for me. He's not only intelligent but incredibly hard-working. He's just finished his sophomore year, having blown the curve in my organic class away and he thinks he wants to be a pharmaceutical chemist. I feel like he is capable of doing incredible work, especially if he stays interested in a project and works on it for the next 2 years. But I don't know what to do with him! I'm so used to having okay students who are happy with okay little projects, and I've been concentrating on administration, that I need help or suggestions or something..... I've been an on and off member of this list and realize that this is not exactly the typical question, but I thought it couldn't hurt to ask. So if you had a willing young worker who wanted to be a pharmaceutical chemist when he grows up what would you have him do? I have Spartan and Gaussian available. He's been playing around with Spartan for the last few weeks. I also am willing to get other programs if there are other types of calculations that people do. I'm also willing to collaborate with someone who's doing pharmaceutical research and thinks they could use us. I don't want to shortchange this student; I'd like to give him a real taste of what pharmaceutical computational chemists do; and I think he's capable of doing really high quality work. Besides, I'd like to learn along with him. Any help or suggestions are welcome. barbara_murray|redlands.edu -- *********************************************************** Barbara Murray barbara_murray|redlands.edu Director The Center for Science and Mathematics University of Redlands Redlands, CA From owner-chemistry@ccl.net Sun May 4 13:36:00 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli===gmail.com" To: CCL Subject: CCL:G: Undergraduate research question Message-Id: <-36888-080504132733-4183-71ka0UC3iFOIbTJDpLj1Zw||server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_3396_18019076.1209922037089" Date: Sun, 4 May 2008 20:27:17 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli.[A].gmail.com] ------=_Part_3396_18019076.1209922037089 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Being a student (undergraduate) interested in molecular modelling (protein modelling specifically) myself, I would say that what he needs first is a general computational chemistry course. After which a general survey book about current topics in this field is what he needs. Once a person with a scientist mind feels some curiosity or even attraction to a certain subject he must then learn the general terms and "jargon" of that branch. After which he starts reading world class journal articles on the matter (to those which he has access to). First half of a year will pass with little udnerstanding after which he will start to really easly grasp them. I have been introduced to molecular modelling one and a half years ago. I got a general course on the topic. During my readings protein folding topic really grasped my attention and now for a masters course I am coding a protein folding simulation program (I am an undergraduate yet). I have really learned most of what I learned from journals but journal reading can sometimes (and usually at the beggining almost always) be frustrating... I am justing reflecting my fresh experiences on the matter. In my opinion choosing a specific topic is really important once he has gotten the basic courses and knowledge on the matter. You should note that also undergraduate is a place for learning basic tools of science which he should take seriously. For a computational chemist, *a very good knowledge* of linear algebra and program coding is important in my opinion. On Sun, May 4, 2008 at 8:09 AM, Barbara Murray barbara_murray~!~redlands.edu< owner-chemistry[A]ccl.net> wrote: > > Sent to CCL by: Barbara Murray [barbara_murray]=[redlands.edu] > Let me give the list some background before I try to ask my question. I > teach organic chemistry at a small private, undergraduate university. I was > trained as a solid state synthetic chemist about 30 years ago. About 15 > years ago I became interested in computational chemistry and have dabbled in > it ever since. I say dabbled because a) although faculty are encouraged to > stay professionally active here, teaching is our first priority (and my > first love) and b) for the last 10 years I've been a half time administrator > so I have little time to do research. > > All of our chemistry majors do at least a senior research project and some > do much more. I've had the occasional student work for me doing what I call > computational studies of biologically active molecules. A student does a > literature search to find a set of biologically interesting molecules that > all work on the same receptor (one example was protease inhibitors when they > were first coming out). The student then uses computational chemistry > (usually electrostatic potentials) and information about the receptor's > active site to determine why one molecule might work better than another. > These are not earth shaking projects (nor publishable), but the students > learn a bit about computational chemistry and I'm generally happy. > > But my problem (or not) is that I now have one of the smartest students > I've had in over 20 years who wants to work for me. He's not only > intelligent but incredibly hard-working. He's just finished his sophomore > year, having blown the curve in my organic class away and he thinks he wants > to be a pharmaceutical chemist. > > I feel like he is capable of doing incredible work, especially if he stays > interested in a project and works on it for the next 2 years. But I don't > know what to do with him! I'm so used to having okay students who are happy > with okay little projects, and I've been concentrating on administration, > that I need help or suggestions or something..... > > I've been an on and off member of this list and realize that this is not > exactly the typical question, but I thought it couldn't hurt to ask. > > So if you had a willing young worker who wanted to be a pharmaceutical > chemist when he grows up what would you have him do? I have Spartan and > Gaussian available. He's been playing around with Spartan for the last few > weeks. I also am willing to get other programs if there are other types of > calculations that people do. I'm also willing to collaborate with someone > who's doing pharmaceutical research and thinks they could use us. I don't > want to shortchange this student; I'd like to give him a real taste of what > pharmaceutical computational chemists do; and I think he's capable of doing > really high quality work. Besides, I'd like to learn along with him. > > Any help or suggestions are welcome. barbara_murray*redlands.edu > > -- > *********************************************************** > Barbara Murray barbara_murray*redlands.edu > Director > The Center for Science and Mathematics > University of Redlands > Redlands, CAhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- "Vectors have never been of the slightest use to any creature. Quaternions came from Hamilton after his really good work had been done; and though beautifully ingenious, have been an unmixed evil to those who have touched them in any way, including Maxwell." - Lord Kelvin ------=_Part_3396_18019076.1209922037089 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Being a student (undergraduate) interested in molecular modelling (pro= tein modelling specifically) myself, I would say that what he needs fi= rst is a general computational chemistry course. After which a general surv= ey book about current topics in this field is what he needs. Once a person = with a scientist mind feels some curiosity or even attraction to a certain = subject he must then learn the general terms and "jargon&quo= t; of that  branch. After which he starts reading world class jou= rnal articles on the matter (to those which he has access to). First half o= f a year will pass with little udnerstanding after which he will start to r= eally easly grasp them. I have been introduced to molecular modelling one a= nd a half years ago. I got a general course on the topic. During my reading= s protein folding topic really grasped my attention and now for a masters c= ourse I am coding a protein folding simulation program (I am an undergradua= te yet). I have really learned most of what I learned from journals but jou= rnal reading can sometimes (and usually at the beggining almost always) be = frustrating... I am justing reflecting my fresh experiences on the matter. = In my opinion choosing a specific topic is really important once he has got= ten the basic courses and knowledge on the matter. You should note that als= o undergraduate is a place for learning basic tools of science which he sho= uld take seriously. For a computational chemist, a very good knowledge of linear algebra and program coding  is important in my = opinion.

On Sun, May 4, 2008 at 8:09 AM, Barbara Murray b= arbara_murray~!~redlands.edu <owner-chemistry[A]ccl.net> wrote:=

Sent to CCL by: Barbara Murr= ay [barbara_murray]=3D[r= edlands.edu]
Let me give the list some background before I try to ask my question.  = ;I teach organic chemistry at a small private, undergraduate university. &n= bsp;I was trained as a solid state synthetic chemist about 30 years ago. &n= bsp;About 15 years ago I became interested in computational chemistry and h= ave dabbled in it ever since.  I say dabbled because a) although facul= ty are encouraged to stay professionally active here, teaching is our first= priority (and my first love) and b) for the last 10 years I've been a = half time administrator so I have little time to do research.

All of our chemistry majors do at least a senior research project and s= ome do much more.  I've had the occasional student work for me doi= ng what I call computational studies of biologically active molecules. &nbs= p;A student does a literature search to find a set of biologically interest= ing molecules that all work on the same receptor (one example was protease = inhibitors when they were first coming out).  The student then uses co= mputational chemistry (usually electrostatic potentials) and information ab= out the receptor's active site to determine why one molecule might work= better than another.  These are not earth shaking projects (nor publi= shable), but the students learn a bit about computational chemistry and I&#= 39;m generally happy.

But my problem (or not) is that I now have one of the smartest students= I've had in over 20 years who wants to work for me.  He's not= only intelligent but incredibly hard-working.  He's just finished= his sophomore year, having blown the curve in my organic class away and he= thinks he wants to be a pharmaceutical chemist.

I feel like he is capable of doing incredible work, especially if he st= ays interested in a project and works on it for the next 2 years.  But= I don't know what to do with him!  I'm so used to having okay= students who are happy with okay little projects, and I've been concen= trating on administration, that I need help or suggestions or something....= .

I've been an on and off member of this list and realize that this i= s not exactly the typical question, but I thought it couldn't hurt to a= sk.

So if you had a willing young worker who wanted to be a pharmace= utical chemist when he grows up what would you have him do?  I have Sp= artan and Gaussian available.  He's been playing around with Spart= an for the last few weeks.  I also am willing to get other programs if= there are other types of calculations that people do.  I'm also w= illing to collaborate with someone who's doing pharmaceutical research = and thinks they could use us.  I don't want to shortchange this st= udent; I'd like to give him a real taste of what pharmaceutical computa= tional chemists do; and I think he's capable of doing really high quali= ty work.  Besides, I'd like to learn along with him.

Any help or suggestions are welcome.  barbara_murray*redlands.edu

--
******= *****************************************************
Barbara Murray &nb= sp;     barbara_murray*redlands.edu
Director
The Center for Science and Mathematics
University of Redland= s
Redlands, CA



-=3D This is automatically added to each m= essage by the mailing script =3D-
To recover the email address of the au= thor of the message, please changelook = up the X-Original-From: line in the mail header.

E-mail to subscribe= rs: CHEMISTRY[A]ccl.ne= t or use:
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message
E-mail to administrators: CHEMISTRY-REQUEST[A]ccl.net or use
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsu= b.shtml

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

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)

I= f your mail bounces from CCL with 5.7.1 error, check:
    http://www.ccl.ne= t/spammers.txt

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




--
"Vectors = have never been of the slightest use to any creature. Quaternions came from= Hamilton after his really good work had been done; and though beautifully = ingenious, have been an unmixed evil to those who have touched them in any = way, including Maxwell." - Lord Kelvin=20 ------=_Part_3396_18019076.1209922037089-- From owner-chemistry@ccl.net Sun May 4 20:25:00 2008 From: "Brian Salter-Duke brian.james.duke()gmail.com" To: CCL Subject: CCL:G: OPT+Freq calculation Message-Id: <-36889-080504191843-4650-MZ732kqUyE/FTta659nByA- -server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 05 May 2008 08:23:14 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke-$-gmail.com] Mike Ramos mikeart9+/-yahoo.com wrote: > Sent to CCL by: "Mike Ramos" [mikeart9]^[yahoo.com] > Hi all, > I have a question regarding the OPT+Freq calculation on a organic dye molecule containing aromatic ring, N and S. > when I perform a combine OPT+Freq calculations using g98 suite I get the following output, however, the job is terminated normally. > > A part of the output is, > Exact polarizability: 460.270 0.017 165.147 -0.011 0.004 83.671 > Approx polarizability: 946.252 0.009 298.846 -0.071 -0.001 135.419 > Full mass-weighted force constant matrix: > Low frequencies --- -13.1622 -9.1671 -0.4072 -0.0102 0.0113 0.0301 > Low frequencies --- 46.4240 76.1170 160.3242 > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), > Raman scattering activities (A**4/AMU), Raman depolarization ratios, > reduced masses (AMU), force constants (mDyne/A) and normal coordinates: > 1 2 3 > ?A ?A ?A > Frequencies -- 46.3783 76.1118 160.3242 > Red. masses -- 6.8205 4.0843 4.7897 > Frc consts -- 0.0086 0.0139 0.0725 > IR Inten -- 6.5969 0.0000 0.0039 > Raman Activ -- 0.0000 0.0000 0.0000 > Depolar -- 0.0000 0.0000 0.0000 > > > The input contains the following command, > # opt freq b3lyp/6-311+g(d) scf=(qc,maxcycle=500,conver=5) geom=connectivity gfinput iop(6/7=3) > > My question is why do I get "?" mark in the output file. Am I making any mistak? > > Gaussian has rather tight criteria for judging the symmetry. I suggest that all is probably well, but have a look at the geometry. What symmetry does the molecule have? Has it strictly kept it. Brian > Thanks in advance > mike> > -- Brian Salter-Duke (Brian Duke) Brian.James.Duke#gmail.com Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.