From owner-chemistry@ccl.net Mon May 10 05:19:00 2010 From: "Jens Spanget-Larsen spanget/./ruc.dk" To: CCL Subject: CCL: Method for Hydrogen Bonding Message-Id: <-41831-100510041137-24093-EJ4m2V8823Mu+aqG9j+44A(!)server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 10 May 2010 10:11:25 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget() ruc.dk] Dear Sanjay, the answer to your question depends to some extent on the properties yopu wish to describe: Molecular geometry, energy, spectroscopic transitions? - A comparison of DFT and PM2 results for intramolecularly H-bonded malonaldehyde enol can be found in Spanget-Larsen: Chemical Physics 240, 51-61 (1999). 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 ------------------------------------------------------ Sanjay Bharathwaj computationalchemist.:.gmail.com wrote: > Dear Friends, > > Could you please let me know the methods > either HF, DFT (if so which functional) that helps > me to study the hydrogen bonded interaction. > > I find from literatures, that MP2/Lanl2dz provides > the best.But i think it takes me long time for my system. > In this regard, could you please let me know any other > methods (computationally cheap) that help me to > solve the problem. > > best regards, > Sanjay > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > Andhra pradhesh, > India. From owner-chemistry@ccl.net Mon May 10 09:23:01 2010 From: "Kshatresh Dutta Dubey kshatresh!^!gmail.com" To: CCL Subject: CCL: Interpretation of HOMO and LUMO energy values Message-Id: <-41832-100510035933-4783-g+bOJAsHUFZje39bJoPcpg]-[server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=0016362849e083a0cc048638c969 Date: Mon, 10 May 2010 13:29:23 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh/a\gmail.com] --0016362849e083a0cc048638c969 Content-Type: text/plain; charset=ISO-8859-1 Dear all, I am simulating a protein ligand complex by QM/MM method. I got HOMO = 0.0171 and LUMO = 0.1507 for ligand in bound state. For isolated ligand in unbound state i got HOMO=* -*0.1977 and LUMO= -0.0518. I am unable to interpret this result. Kindly help me to resolve this problem. Thanks in advance Kshatresh Dutta Dubey --0016362849e083a0cc048638c969 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,

I am simulating a protein ligand complex by QM/MM method. = I got HOMO =3D 0.0171 and LUMO =3D 0.1507 for ligand in bound state. For is= olated ligand in unbound state i got HOMO=3D -0.1977 and LUMO=3D -0.= 0518. I am unable to interpret this result. Kindly help me to resolve this = problem.
Thanks in advance

Kshatresh Dutta Dubey
--0016362849e083a0cc048638c969-- From owner-chemistry@ccl.net Mon May 10 09:58:00 2010 From: "Gerard Pujadas gerard.pujadas/./gmail.com" To: CCL Subject: CCL: Step by step instructions for installing OpenEye software in Ubuntu 10.04 and 9.10 Message-Id: <-41833-100510062358-16406-uOWDocxg9r0n7dZFHIIIsw(_)server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=000325558e16dcc66504863acdf9 Date: Mon, 10 May 2010 12:23:46 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas+*+gmail.com] --000325558e16dcc66504863acdf9 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL list members, this weekend I have been successful running the latest OpenEye software versions with Ubuntu 10.04 and 9.10 (64 bits) and I think that the "how to do" information can be of help for some of you [I have used some information that kindly provided to me Vincent Leroux, Greg Warren and Joe Corkery to my question to the CCL list "Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?" last 29/10/2009]: *1)* Download the SuSE v9.1 x86_64 software packages from the OpenEye website. In my case, I download the next packages: babel-3.3-suse-9.1-x86_64.tar.gz eon-2.0.1-suse-9.1-x86_64.tar.gz filter-2.0.2-suse-9.1-x64.tar.gz fred-2.2.5-suse-9.1-x64.tar.gz ogham-1.7.0-suse-9.1-x64.tar.gz omega-2.3.2-suse-9.1-x64.tar.gz quacpac-1.3.1-suse-9.1-x64.tar.gz rocs-3.0.0-suse-9.1-x64.tar.gz szybki-1.3.4-suse-9.1-x64.tar.gz vida-4.0.0-suse-9.1-x64.tar.gz *2)* Download the RedHat Enterprise x86_64 software package from brood brood-2.0.0-redhat-RHEL3-x64.tar.gz *3)* Uncompress, for instance, *eon-2.0.1-suse-9.1-x86_64.tar.gz* in your Desktop. This will create an *openeye* folder that, in my case, I have moved to my */home/gerard/MolBioSoft* folder. *4)* Next, uncompress a second .tar.gz package in your Desktop (for instance *filter-2.0.2-suse-9.1-x64.tar.gz*). Again, an *openeye* folder will be created in your Desktop. Move this *openeye* folder to the parent folder of the previous *openeye* folder that contains yet *EON* (in my case, the * /home/gerard/MolBioSoft* folder) and when the graphical interface ask you how to manage a second *openeye* folder within */home/gerard/MolBioSoft*select the *combine* option. This will merge the contents of the *openeye* folder obtained by uncompress *eon-2.0.1-suse-9.1-x86_64.tar.gz* and * filter-2.0.2-suse-9.1-x64.tar.gz*. Proceed with the same protocol for the rest of packages. *5)* Put your *oe_license.txt* license document into the resulting *openeye*folder (in my case */home/gerard/MolBioSoft/openeye*) *6)* Edit your *bash.bashrc* configuration file (use the *sudo -s gedit /etc/bash.bashrc* command) and add at its end the next information (please replace */home/gerard/MolBioSoft/* in the next line by the absolute path of your *openeye* folder): export OE_DIR=/home/gerard/MolBioSoft/openeye export OE_ARCH=suse-9.1-x64 alias align="$OE_DIR/bin/align" alias brood="$OE_DIR/arch/redhat-RHEL3-x64/brood/2.0.0/brood" alias checkcff="$OE_DIR/bin/checkcff" alias chunker="$OE_DIR/bin/chunker" alias depict="$OE_DIR/bin/depict" alias eon="$OE_DIR/bin/eon" alias filter="$OE_DIR/bin/filter" alias fixpka="$OE_DIR/bin/fixpka" alias flipper="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/flipper" alias fred="$OE_DIR/bin/fred" alias hlmerge="$OE_DIR/bin/hlmerge" alias makefraglib="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/makefraglib" alias makerocsdb="$OE_DIR/bin/makerocsdb" alias mol2gif="$OE_DIR/bin/mol2gif" alias mol2img="$OE_DIR/bin/mol2img" alias mol2ps="$OE_DIR/bin/mol2ps" alias molcharge="$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/molcharge" alias molprop="$OE_DIR/bin/molprop" alias oeb2sdconf="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/oeb2sdconf" #alias oempirun="$OE_DIR/bin/oempirun" alias omega="$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/omega2" alias openeyebabel="$OE_DIR/bin/openeyebabel" #alias orted="$OE_DIR/bin/orted" alias picto="$OE_DIR/bin/picto" alias pkatyper="$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/pkatyper" alias rocs="$OE_DIR/bin/rocs" alias szybki="$OE_DIR/bin/szybki" alias tautomers="$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/tautomers" alias vbrood="$OE_DIR/arch/redhat-RHEL3-x64/brood/2.0.0/vbrood" alias vida="$OE_DIR/bin/vida" alias vrocs="$OE_DIR/bin/vrocs" Save and close the */etc/bash.bashrc* document *7)* In order to know if *vida* runs, open a new terminal (or write the *source /etc/bash.bashrc* command in a yet opened terminal) and write *vida*. In my case, the next error message occurs: gerard{:}URV-nutrigenomica-01:~$ vida /home/gerard/MolBioSoft/openeye/arch/suse-9.1-x64/vida/4.0.0/bin/vida: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory gerard{:}URV-nutrigenomica-01:~$ This means that the libstdc++.so.5 is not in my Ubuntu distribution (and it seems that this library has been dropped from the latest Ubuntu distributions ...). Then, I have followed the instructions at http://www.digitalenigma.com/directory.php?include=home Basically they consist on writing the next commands in the command line: mkdir /tmp/libstdc++5 cd /tmp/libstdc++5 wget http://mirrors.kernel.org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_amd64.deb wget http://mirrors.kernel.org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_i386.deb sudo updatedb locate libstdc++.so. sudo dpkg --force-architecture -i libstdc++5_3.3.6-17ubuntu1_i386.deb sudo updatedb locate libstdc++.so. sudo mv /usr/lib/libstdc++.so.5* /usr/lib32/. sudo updatedb locate libstdc++.so. sudo dpkg -i libstdc++5_3.3.6-17ubuntu1_amd64.deb sudo updatedb locate libstdc++.so. *8)* Try again if *vida* runs by writing the *vida* command in a new terminal (or in the same one where you write the the *source /etc/bash.bashrc* command after updating * /etc/bash.bashrc* information). In my case, the next error message occurs: gerard{:}URV-nutrigenomica-01:~$ vida /home/gerard/MolBioSoft/openeye/arch/suse-9.1-x64/vida/4.0.0/bin/vida: error while loading shared libraries: libpng.so.3: cannot open shared object file: No such file or directory gerard{:}URV-nutrigenomica-01:~$ Then, you need to know which is the current version you have of the *libpng*library in your computer and use it to make a symbolic link with the filename *libpng.so.3* at the */usr/lib* folder. Thus, in order to know which is the version you have of the *libpng* library open the *synaptic*utility and search for the *libpng* filename. In my case, I see that the *libpng* library I have is * libpng12-0*. Push the *libpng12-0* row in *synaptic* with your right-mouse button and select *Properties* in order to see where is the library installed and which is exactly its filename. In the resulting window, select the *Installed files* tab and take a look to the filenames it shows. In my case, its name is *libpng12.so.0.42.0* and it is installed at the */lib*folder. Then, I have written the *sudo ln -s /lib/libpng12.so.0.42.0 /usr/lib/libpng.so.3* command in the terminal: gerard{:}URV-nutrigenomica-01:~$ sudo ln -s /lib/libpng12.so.0.42.0 /usr/lib/libpng.so.3 and now I tried again to run *vida* by writing the *vida* command in a new terminal (or in the same one where you write the the *source /etc/bash.bashrc* command after updating * /etc/bash.bashrc* information) and, it works now (and also picto, vrocs and vbrood) !!! Hope this helps Best Gerard -- Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 Nutrigenomics Research Group Biochemistry and Biotechnology Department Universitat Rovira i Virgili Tarragona, Catalonia --000325558e16dcc66504863acdf9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL list members,

this weekend I have been successful runni= ng the latest OpenEye software versions with Ubuntu 10.04 and 9.10 (64 bits= ) and I think that the "how to do" information can be of help for= some of you [I have used some information that kindly provided to me Vince= nt Leroux, Greg Warren and Joe Corkery to my question to the CCL list "= ;Do ROCS and VIDA (from OpenEye) work with the 64bits version of Ubuntu?&qu= ot; last 29/10/2009]:

1) Download the SuSE v9.1 x86_= 64 software packages from the OpenEye website. In my case, I download the n= ext packages:

babel-3.3-suse-9.1-x= 86_64.tar.gz
eon-2.0.1-suse-9.1-x86_64.tar.gz
filter-2.0.2-suse-9.1-x64.tar.gz
fre= d-2.2.5-suse-9.1-x64.tar.gz
ogham-1.7.0-suse-9.1-x64.tar.gz
omega-2.3= .2-suse-9.1-x64.tar.gz
quacpac-1.3.1-suse-9.1-x64.tar.gz
rocs-3.0.0-s= use-9.1-x64.tar.gz
szybki-1.3.4-suse-9.1-x64.tar.gz
vida-4.0.0-suse-9.1-x64.tar.gz

2) Download the RedHat Enterprise x86_64 software package from = brood

brood-2.0.0-redhat-RHEL3-x64= .tar.gz

3) Uncompress, for instance, eon-2.0.1-suse-9.1-x86_64.= tar.gz in your Desktop. This will create an openeye folder that,= in my case, I have moved to my /home/gerard/MolBioSoft folder.

4) Next, uncompress a second .tar.gz package in your Desktop (fo= r instance filter-2.0.2-suse-9.1-x64.tar.gz). Again, an openeye folder will be created in your Desktop. Move this openeye folder = to the parent folder of the previous openeye folder that contains ye= t EON (in my case, the /home/gerard/MolBioSoft folder) and wh= en the graphical interface ask you how to manage a second openeye fo= lder within /home/gerard/MolBioSoft select the combine option= . This will merge the contents of the openeye folder obtained by unc= ompress eon-2.0.1-suse-9.1-x86_64.tar.gz and filter-2.0.2-suse-= 9.1-x64.tar.gz. Proceed with the same protocol for the rest of packages= .

5) Put your oe_license.txt license document into the resu= lting openeye folder (in my case /home/gerard/MolBioSoft/openeye<= /b>)

6) Edit your bash.bashrc configuration file (use = the sudo -s gedit /etc/bash.bashrc command) and add at its end the n= ext information (please replace /home/gerard/MolBioSoft/ in the next= line by the absolute path of your openeye folder):

export OE_DIR=3D/home/gerard/Mo= lBioSoft/openeye
export=20 OE_ARCH=3Dsuse-9.1-x64

alias align=3D"$OE_DIR/bin/align"alias=20 brood=3D"$OE_DIR/arch/redhat-RHEL3-x64/brood/2.0.0/brood"
alia= s=20 checkcff=3D"$OE_DIR/bin/checkcff"
alias chunker=3D"$OE_DIR/bin/chunker"
alias depict=3D"$OE= _DIR/bin/depict"
alias eon=3D"$OE_DIR/bin/eon"
alias filter=3D"$OE_DIR/bin/filt= er"
alias=20 fixpka=3D"$OE_DIR/bin/fixpka"
alias flipper=3D"$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/flipper"alias fred=3D"$OE_DIR/bin/fred"
alias hlmerge=3D"$OE_DIR/bin/h= lmerge"
alias makefraglib=3D"$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/makefraglib"= ;
alias makerocsdb=3D"$OE_DIR/bin/makerocsdb"
alias=20 mol2gif=3D"$OE_DIR/bin/mol2gif"
alias mol2img=3D"$OE_DIR/= bin/mol2img"
alias mol2ps=3D"$OE_DIR/bin/mol2ps"
alias molcharge=3D"$OE_DIR= /arch/suse-9.1-x64/quacpac/1.3.1/bin/molcharge"
alias molprop=3D"$OE_DIR/bin/molprop"
alias=20 oeb2sdconf=3D"$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/oeb2sdconf"#alias oempirun=3D"$OE_DIR/bin/oempirun"
alias=20 omega=3D"$OE_DIR/arch/suse-9.1-x64/omega/2.3.2/omega2"
alias openeyebabel=3D"$OE_DIR/bin/openeyebabel"
#alias=20 orted=3D"$OE_DIR/bin/orted"
alias picto=3D"$OE_DIR/bin/pi= cto"
alias=20 pkatyper=3D"$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/pkatyper"=
alias rocs=3D"$OE_DIR/bin/rocs"
alias szybki=3D"$OE_DIR/b= in/szybki"
alias tautomers=3D"$OE_DIR/arch/suse-9.1-x64/quacpac/1.3.1/bin/tautomers&qu= ot;
alias vbrood=3D"$OE_DIR/arch/redhat-RHEL3-x64/brood/2.0.0/vbrood"
alias vida=3D"$OE_DIR/bin/vida"
alias vrocs=3D"$OE_DIR/bi= n/vrocs"

Save and close the /etc/bash.bashrc docum= ent

7) In order to know if vida runs, open a new termi= nal (or write the source /etc/bash.bashrc command in a yet opened te= rminal) and write vida. In my case, the next error message occurs:
gerard{:}URV-nutrigenomica-01:~$ vida/home/gerard/MolBioSoft/openeye/arch/suse-9.1-x64/vida/4.0.0/bin/vida: er= ror while loading shared libraries: libstdc++.so.5: cannot open shared obje= ct file: No such file or directory
gerard{:}URV-nutrigenomica-01:~$

This means that the libstdc++.s= o.5 is not in my Ubuntu distribution (and it seems that this library has be= en dropped from the latest Ubuntu distributions ...). Then, I have followed= the instructions at http://www.digitalenigma.com/directory.ph= p?include=3Dhome

Basically they consist on writing the next commands in the command line= :

mkdir /tmp/libstdc++5
cd /tmp/libstdc++5
wget http://mirrors.kernel= .org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_amd64.deb
wget http://mirrors.kernel.= org/ubuntu/pool/universe/g/gcc-3.3/libstdc++5_3.3.6-17ubuntu1_i386.deb<= br> sudo updatedb
locate libstdc++.so.

sudo dpkg=20 --force-architecture -i libstdc++5_3.3.6-17ubuntu1_i386.deb
sudo updatedb
locate libstdc++.so.
sudo mv /usr/lib/libstdc++.so.5*=20 /usr/lib32/.
sudo updatedb
locate libstdc++.so.

sudo dpkg -i libstdc++5_3.3.6-17ubuntu1_amd64.d= eb
sudo updatedb
locate libstdc++.so.

8) Try again if vi= da runs by writing the vida command in a new terminal (or in the= same one where you write the the source /etc/bash.bashrc command af= ter updating=A0 /etc/bash.bashrc information). In my case, the next = error message=20 occurs:

gerard{:}URV-nutrigenomica-0= 1:~$ vida
/home/gerard/MolBioSoft/openeye/arch/suse-9.1-x64/vida/4.0.0/b= in/vida: error while loading shared libraries: libpng.so.3: cannot open sha= red object file: No such file or directory
gerard{:}URV-nutrigenomica-01:~$

Then, you need to know which is= the current version you have of the libpng library in your computer= and use it to make a symbolic link with the filename libpng.so.3 at= the /usr/lib folder. Thus, in order to know which is the version yo= u have of the libpng library open the synaptic utility and se= arch for the libpng filename. In my case, I see that the libpng library I have is libpng12-0. Push the libpng12-0 row in <= b>synaptic with your right-mouse button and select Properties in= order to see where is the library installed and which is exactly its filen= ame. In the resulting window, select the Installed files tab and tak= e a look to the filenames it shows. In my case, its name is libpng12.so.= 0.42.0 and it is installed at the /lib folder. Then, I have writ= ten the sudo ln -s /lib/libpng12.so.0.42.0 /usr/lib/libpng.so.3 comm= and in the terminal:

gerard{:}URV-nutrigenomica-01:~$ sudo l= n -s /lib/libpng12.so.0.42.0 /usr/lib/libpng.so.3

and now I tr= ied again to run vida by writing the vida command in a new te= rminal (or in the same one where you write the the source /etc/bash.bashrc command after=20 updating=A0 /etc/bash.bashrc information) and, it works now (and als= o picto, vrocs and vbrood) !!!


Hope this helps

Best

Gerard

--
Gerard Puja= das
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigen= omics Research Group
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia
--000325558e16dcc66504863acdf9-- From owner-chemistry@ccl.net Mon May 10 10:33:00 2010 From: "Iain Moal Iain.Moal . cancer.org.uk" To: CCL Subject: CCL: Modify PDB file of DNA-Protein complexes Message-Id: <-41834-100510052940-23993-Q273KA54uBemTnHAVaNKSg*server.ccl.net> X-Original-From: "Iain Moal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CAF023.11172211" Date: Mon, 10 May 2010 10:26:03 +0100 MIME-Version: 1.0 Sent to CCL by: "Iain Moal" [Iain.Moal,+,cancer.org.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01CAF023.11172211 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CHARMM can do this for you, using the IC Build command. -----Original Message----- > From: owner-chemistry+iain.moal=3D=3Dcancer.org.uk:-:ccl.net on behalf of De= epa Pandit Deepangi.Pandit|gmail.com Sent: Sat 08/05/2010 22:11 To: Iain Moal Subject: CCL: Modify PDB file of DNA-Protein complexes =20 Sent to CCL by: "Deepa Pandit" [Deepangi.Pandit=3D=3D=3Dgmail.com] Hi: I would like to modify an existing PDB file of the protein-DNA complex in = such a way that only bases are changed. I would like to keep the phosphate= backbone of the DNA unchanged (if possible) and protein structure remains= unchanged. What kind of software/server/program is suitable to perform th= e task?=20 I came across 3D-DART but it is useful for building DNA. Not sure how to a= ddress the protein issue. http://haddock.chem.uu.nl/dna/DARTusage.html#buildna Thank you. Deepa -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cance= rresearchuk.org. We are a charity registered under number 1089464 and a co= mpany limited by guarantee registered in England & Wales under number 4325= 234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. O= ur central telephone number is 020 7242 0200. =20 This communication and any attachments contain information which is confid= ential and may also be privileged. It is for the exclusive use of the in= tended recipient(s). If you are not the intended recipient(s) please note= that any form of disclosure, distribution, copying or use of this communi= cation or the information in it or in any attachments is strictly prohibit= ed and may be unlawful. If you have received this communication in error,= please notify the sender and delete the email and destroy any copies of i= t. =20 E-mail communications cannot be guaranteed to be secure or error free, as = information could be intercepted, corrupted, amended, lost, destroyed, arr= ive late or incomplete, or contain viruses. We do not accept liability fo= r any such matters or their consequences. Anyone who communicates with us= by e-mail is taken to accept the risks in doing so. ------_=_NextPart_001_01CAF023.11172211-- From owner-chemistry@ccl.net Mon May 10 11:08:00 2010 From: "Vaibhav Jain vaibhav_pharmacy-.-yahoo.co.in" To: CCL Subject: CCL:G: Help on G03 error: "Incomplete coordinate system" Message-Id: <-41835-100510092930-29578-njH0pmGbMe1Dg9Fnm0v9ww/./server.ccl.net> X-Original-From: "Vaibhav Jain" Date: Mon, 10 May 2010 09:29:29 -0400 Sent to CCL by: "Vaibhav Jain" [vaibhav_pharmacy_+_yahoo.co.in] Dear all, I'm getting a recurrent error during geometry optimization (PM3 level) jobs, using Gaussian G03W. I can't figure out what this error means and couldn't find any helping information on the manuals or the web. So I'm hopping someone from this forum could have any helpful hint. The system I'm studying is composed of tetramer ie. two dimer system stabilized by interaction with HCl. The optimization runs apparently OK for a number of steps, but eventually it stops with the following message Incomplete coordinate system. Try restarting with Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Incomplete coordinate system. Error termination via Lnk1e in /opt/g03/l103.exe at Mon May 10 14:27:33 2010. Job cpu time: 0 days 0 hours 17 minutes 34.1 seconds. File lengths (MBytes): RWF= 64 Int= 0 D2E= 0 Chk= 47 Scr= 1 r= Pls help me solve this error... Thanks vaibhav From owner-chemistry@ccl.net Mon May 10 11:53:00 2010 From: "Elaine Meng meng=cgl.ucsf.edu" To: CCL Subject: CCL: Modify PDB file of DNA-Protein complexes Message-Id: <-41836-100509131303-21822-dooTuAfihat7FlqG4NoVUg%server.ccl.net> X-Original-From: "Elaine Meng" Date: Sun, 9 May 2010 13:13:01 -0400 Sent to CCL by: "Elaine Meng" [meng||cgl.ucsf.edu] Hi Deepangi, You can do it with the "swapna" command in Chimera. Chimera homepage: http://www.cgl.ucsf.edu/chimera/index.html Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html manual page for "swapna": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html Example commands: open 1d86 nuc side atoms swapna t :24.b (that would open PDB 1d86, show all atoms of bases, and change the base of residue 24 in chain B to T) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Mon May 10 13:29:00 2010 From: "Austin Yongye ayongye]^[gmail.com" To: CCL Subject: CCL: geometry vs wavefunction convergence Message-Id: <-41837-100510104356-18361-Rr4o5aWi4ZjsqLT0dVNTgw-.-server.ccl.net> X-Original-From: "Austin Yongye" Date: Mon, 10 May 2010 10:43:54 -0400 Sent to CCL by: "Austin Yongye" [ayongye%x%gmail.com] Hi CCLers, I performed restraint-free geometry optimizations using four rotamers of the same molecule. The optimizations all converged, essentially to the same structure: superposition, bond lengths, angles and dihedral angles. The problem is that the energy difference between the most and least stable structures is about 5 kcal/mol. Could this be due to differences in the final wavefunctions of the rotamers? I'm using b3lyp/6-31G*//b3lyp/3-21G* in toluene. Thanks, Austin- From owner-chemistry@ccl.net Mon May 10 14:04:00 2010 From: "Subhendu Roy subhendu.roi . gmail.com" To: CCL Subject: CCL: Frequency calculation unsuccessful in G09 Message-Id: <-41838-100510051330-4787-Rr4o5aWi4ZjsqLT0dVNTgw#server.ccl.net> X-Original-From: "Subhendu Roy" Date: Mon, 10 May 2010 05:13:29 -0400 Sent to CCL by: "Subhendu Roy" [subhendu.roi=gmail.com] Dear Sir, I was doing the frequency calculation of the following input(important part of it is shown below)in G09: %chk=zr-bas-freq.chk %nprocshared=8 %nproclinda=2 %mem=400MW # bp86/gen freq nosymm pseudo=read Title 0 1 C 3.173372000 13.395230000 10.497352000 H 2.966896000 13.232882000 11.553091000 .... The calculation was going on properly but suddenly it came out showing the following message: 7 vectors produced by pass155 Test12= 1.39D-13 1.00D-09 XBig12= 1.14D-14 2.89D-09. 7 vectors produced by pass156 Test12= 1.39D-13 1.00D-09 XBig12= 8.68D-15 2.34D-09. 7 vectors produced by pass157 Test12= 1.39D-13 1.00D-09 XBig12= 7.72D-15 2.35D-09. 7 vectors produced by pass158 Test12= 1.39D-13 1.00D-09 XBig12= 6.56D-15 1.95D-09. 5 vectors produced by pass159 Test12= 1.39D-13 1.00D-09 XBig12= 2.94D-15 1.34D-09. Applied DIIS recursively to reduced A of dimension 5268. failed to open execfile I got these type of unsuccessful terminations for two of my frequency jobs. Can someone please help me in figuring out the problem? Thank you in advance. Best regards, Subhendu Roy, IISc, Bangalore, India From owner-chemistry@ccl.net Mon May 10 15:02:00 2010 From: "Aleksey Kuznetsov AlexKuznetsov2007 ~ yandex.ru" To: CCL Subject: CCL:G: problem with SCRF optimisation Message-Id: <-41839-100510150003-11236-rgdtRW78hppdn7FkVAd1QQ^server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 10 May 2010 22:59:52 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007%x%yandex.ru] Dear Brian, thank you very much, too, for this advice! Best regards, Aleksey. 07.05.10, 21:48, "Bennion, Brian Bennion1^-^llnl.gov" : > > Sent to CCL by: "Bennion, Brian" [Bennion1%llnl.gov] > Hello, > > Even slight modifications in the sphere radii governed by the "alpha" keyword can help get past these sticky points in G03. > In some publications this parameter is altered for charged species to obtain better results. > > Brian > ------------------------------------------- Dr. Aleksey Kuznetsov Department of Chemistry Duke University 124 Science Dr. Box 90354 Durham, NC 27708-0354 USA Phone: (919) 660-1634 Email: aleksey.kuznetsov],[duke.edu -------------------------------------------