From owner-chemistry@ccl.net Wed Nov 24 04:42:01 2010 From: "MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es" To: CCL Subject: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43209-101124042136-17324-M1KRsGzBEzK7GaR5QiBFzw#%#server.ccl.net> X-Original-From: "MASLYK, MACIEJ MARCIN" Content-Language: pl-PL Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 24 Nov 2010 10:20:47 +0100 MIME-Version: 1.0 Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) regards Maciek ________________________________________ Od: owner-chemistry+maciejmarcin.maslyk==ceu.es!A!ccl.net [owner-chemistry+maciejmarcin.maslyk==ceu.es!A!ccl.net] w imieniu Abrash, Sam sabrash:_:richmond.edu [owner-chemistry!A!ccl.net] Wys³ano: 23 listopada 2010 19:09 Do: MASLYK, MACIEJ MARCIN Temat: CCL:G: Gaussian output problem Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu] Hi, I think David is correct. However, there's a relatively easy fix (I think) unless your atom count exceeds 9999 by a lot. Just go into the output file with an editor, and replace the **** by the actual atom number. That should fix the problem of not being able to read structures (unless the program you're using for the structures has the same problem). Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash]|[richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon. After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu]|[ccl.net [mailto:owner-chemistry+sabrash==richmond.edu]|[ccl.net] On Behalf Of Close, David M. CLOSED _ mail.etsu.edu Sent: Tuesday, November 23, 2010 11:18 AM To: Abrash, Sam Subject: CCL:G: Gaussian output problem Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu] Maciej: Do you own the source code? If so, look at the print command. The program is most likely trying to print a 5 digit number in a fix field (something like I4). Much of Gaussian code is in Fortran with fixed formats. The **** just mean that you have tried to print something that doesn't fix in the space allowed. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es Sent: Tuesday, November 23, 2010 8:45 AM To: Close, David M. Subject: CCL:G: Gaussian output problem Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] Hi everyone, could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? It looks like this in output: 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 **** 8 20001021 23.735956 -43.072924 13.135294 **** 1 20001030 23.388276 -42.182008 13.115359 **** 1 20001030 22.974070 -43.624340 13.312930 Do you have any suggestions? Thanks in advance Maciekhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 24 07:48:00 2010 From: "Close, David M. CLOSED{=}mail.etsu.edu" To: CCL Subject: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43210-101124074653-1381-HRt02wi6rU1oYmJTjOJirw.@.server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 24 Nov 2010 12:46:47 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED*mail.etsu.edu] Maciej: That's easy. One can purchase a program that is already compiled for a specific operating system. If you look at the Gaussian homepage you can select LINUX, WINDOWS, and a variety of parallel versions. These programs can be installed with simple instructions on specific machines. These packages are called machine language binaries. As such you cannot read the code. The other option is to purchase the actual program code (as in Fortran). These programs have to be compiled (or converted into binary code), and then installed on the computer. This option is for people who are developing code, or who are impatient with the numerous bugs that are in most programs. Therefore my original suggestion to your problem was to look at the Fortran code and find the line that prints the output. Most likely it calls for the atom number to be printed in fixed 4 space field (I4), that you could easily try to fix. As someone else pointed out, in another subroutine that used this output, you could cause a new problem with this altered format. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu _ ccl.net [mailto:owner-chemistry+closed==etsu.edu _ ccl.net] On Behalf Of MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es Sent: Wednesday, November 24, 2010 4:21 AM To: Close, David M. Subject: CCL:G: ODP: CCL:G: Gaussian output problem Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) regards Maciek ________________________________________ Od: owner-chemistry+maciejmarcin.maslyk==ceu.es-x-ccl.net [owner-chemistry+maciejmarcin.maslyk==ceu.es-x-ccl.net] w imieniu Abrash, Sam sabrash:_:richmond.edu [owner-chemistry-x-ccl.net] Wys³ano: 23 listopada 2010 19:09 Do: MASLYK, MACIEJ MARCIN Temat: CCL:G: Gaussian output problem Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu] Hi, I think David is correct. However, there's a relatively easy fix (I think) unless your atom count exceeds 9999 by a lot. Just go into the output file with an editor, and replace the **** by the actual atom number. That should fix the problem of not being able to read structures (unless the program you're using for the structures has the same problem). Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash]|[richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon. After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu]|[ccl.net [mailto:owner-chemistry+sabrash==richmond.edu]|[ccl.net] On Behalf Of Close, David M. CLOSED _ mail.etsu.edu Sent: Tuesday, November 23, 2010 11:18 AM To: Abrash, Sam Subject: CCL:G: Gaussian output problem Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu] Maciej: Do you own the source code? If so, look at the print command. The program is most likely trying to print a 5 digit number in a fix field (something like I4). Much of Gaussian code is in Fortran with fixed formats. The **** just mean that you have tried to print something that doesn't fix in the space allowed. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es Sent: Tuesday, November 23, 2010 8:45 AM To: Close, David M. Subject: CCL:G: Gaussian output problem Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] Hi everyone, could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? It looks like this in output: 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 **** 8 20001021 23.735956 -43.072924 13.135294 **** 1 20001030 23.388276 -42.182008 13.115359 **** 1 20001030 22.974070 -43.624340 13.312930 Do you have any suggestions? Thanks in advance Maciekhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Nov 24 08:29:00 2010 From: "Andrew Voronkov drugdesign||yandex.ru" To: CCL Subject: CCL: multiple conformations analysis free\open source\academic free software Message-Id: <-43211-101124081503-2141-zwxlylMK3b9sGGL1b1pDJA _ server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 24 Nov 2010 16:14:53 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[]yandex.ru] Dear CCL users, I have the next goal - to study multiple conformations of the compounds and check the correlation with the biological activity. I'd like to cluster let's say top 50 conformations and divide them into similarity clusters as well as get representative and\or average structures for each of the clusters. Is there any software which can help me with this? The conformations were generated using Frog2 server. Best regards, Andrew From owner-chemistry@ccl.net Wed Nov 24 09:03:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek-*-few.vu.nl" To: CCL Subject: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43212-101124083349-4835-wVyHGiFQEfUrpTWJ8TpocA===server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 Nov 2010 14:33:42 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek##few.vu.nl] 2010/11/24 MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es : > > Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] > Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? > > Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) You should absolutely complain to Gaussian Inc, this is a bug in their program. However, to actually solve the problem (if you don't have access to the Gaussian source core and/or don't want to rerun your calculation) you can write a simple script that counts the lines and replaces the stars with the correct number. If you don't know how to write such a script and you intend to do more work using this type of quantum chemistry software you should definitely learn to use a scripting laguage such as Python (www.python.org). For someone who knows scripting it's less than an hour of work to fix the problem. If your are lucky some student will already know how to do this. If everything else fails send me an email and I will do it for a modest fee :-) Regards, Ulf Ekstrom From owner-chemistry@ccl.net Wed Nov 24 09:38:00 2010 From: "Esteban Gabriel Vega Hissi egvega,gmail.com" To: CCL Subject: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43213-101124090635-536-TW8n5tYSVirULjlvc+WWDA+*+server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=20cf3054a2e9a366980495ccfe3e Date: Wed, 24 Nov 2010 11:06:04 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega() gmail.com] --20cf3054a2e9a366980495ccfe3e Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: quoted-printable Dear Maciek, I would try making a python, perl, or bash script that: 1) open the output file 2) search for the first line of the structure and step you're interested in (or a line with some "keyword" next to the beginning of the structure) 3) read the structure line by line counting the atom number in a variable and when the "****" appears change them by the following variable number i.e. 10000 and so on writing each line to a log/output file In python, step 3 would by something like this: n_at=3D 15000 #total number of atoms of your structure i=3D1 while i<=3Dn_at: line=3Dfile_in.readline() subline=3Dline.split() if i<9999: file_out.write(line) else: subline[0]=3Dstr(i) file_out.write("%s "*len(subline)%tuple(subline)) i=3Di+1 (NOTE: please, check spelling and identation) Best Esteban G Vega-Hissi UNSL Argentina -- 2010/11/24 Close, David M. CLOSED{=3D}mail.etsu.edu > > Sent to CCL by: "Close, David M." [CLOSED*mail.etsu.edu] > Maciej: > That's easy. One can purchase a program that is already compiled for a > specific operating system. If you look at the Gaussian homepage you can > select LINUX, WINDOWS, and a variety of parallel versions. These program= s > can be installed with simple instructions on specific machines. These > packages are called machine language binaries. As such you cannot read t= he > code. > The other option is to purchase the actual program code (as in Fortran). > These programs have to be compiled (or converted into binary code), and > then installed on the computer. This option is for people who are > developing code, or who are impatient with the numerous bugs that are in > most programs. > Therefore my original suggestion to your problem was to look at the > Fortran code and find the line that prints the output. Most likely it ca= lls > for the atom number to be printed in fixed 4 space field (I4), that you > could easily try to fix. As someone else pointed out, in another subrout= ine > that used this output, you could cause a new problem with this altered > format. > Regards, Dave Close. > > -----Original Message----- > > From: owner-chemistry+closed=3D=3Detsu.edu[a]ccl.net [mailto: > owner-chemistry+closed =3D=3Detsu.edu[a]ccl.net= ] On > Behalf Of MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es > Sent: Wednesday, November 24, 2010 4:21 AM > To: Close, David M. > Subject: CCL:G: ODP: CCL:G: Gaussian output problem > > > Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] > Thanks for help but I'm completely begginer in gaussian and also in linux > so can you guys explain this thing with source code more precisely, pleas= e? > > Sam, I got 15 k atoms and 250 steps so it will kill me if I start changin= g > stars to numbers manually :) > > regards > > Maciek > ________________________________________ > Od: owner-chemistry+maciejmarcin.maslyk=3D=3Dceu.es-x-ccl.net[owner-chemi= stry+maciejmarcin.maslyk=3D=3D > ceu.es-x-ccl.net] w imieniu Abrash, Sam sabrash:_:richmond.edu [ > owner-chemistry-x-ccl.net] > Wys=B3ano: 23 listopada 2010 19:09 > Do: MASLYK, MACIEJ MARCIN > Temat: CCL:G: Gaussian output problem > > Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu] > Hi, > > I think David is correct. However, there's a relatively easy fix (I thin= k) > unless your atom count exceeds 9999 by a lot. Just go into the output fi= le > with an editor, and replace the **** by the actual atom number. That sho= uld > fix the problem of not being able to read structures (unless the program > you're using for the structures has the same problem). > > Sam > > Samuel A. Abrash > Department of Chemistry > University of Richmond > Richmond, VA 23173 > Phone: 804-289-8248 > Fax: 804-287-1897 > E-mail: sabrash]|[richmond.edu > Web-page: http://www.richmond.edu/~sabrash > "In 1893 Charles Hinton left Japan to become a mathematics instructor at > Princeton University, where he invented a baseball-pitching machine that > used gunpowder to propel the balls, like a cannon. After several acciden= ts, > the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ia= n > Steward and Jack Cohen, The Science of Diskworld III > > > -----Original Message----- > > From: owner-chemistry+sabrash=3D=3Drichmond.edu]|[ccl.net [mailto: > owner-chemistry+sabrash =3D=3Drichmond.edu]|[ > ccl.net] On Behalf Of Close, David M. CLOSED _ mail.etsu.edu > Sent: Tuesday, November 23, 2010 11:18 AM > To: Abrash, Sam > Subject: CCL:G: Gaussian output problem > > > Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu] > Maciej: > Do you own the source code? If so, look at the print command. The > program is most likely trying to print a 5 digit number in a fix field > (something like I4). Much of Gaussian code is in Fortran with fixed > formats. The **** just mean that you have tried to print something that > doesn't fix in the space allowed. > Regards, Dave Close. > > -----Original Message----- > > From: owner-chemistry+closed=3D=3Detsu.edu__ccl.net [mailto: > owner-chemistry+closed =3D=3Detsu.edu__ccl.net]= On > Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es > Sent: Tuesday, November 23, 2010 8:45 AM > To: Close, David M. > Subject: CCL:G: Gaussian output problem > > > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > Hi everyone, > could you help me with one problem, please? Every time I'm running G03 jo= b > I got problem with outputs. The problem is that I cannot extract structur= es > because there are stars **** instead of atom numbers higher than 9999. Ha= ve > you ever had this problem in your calculation if you had more than 9999 > atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? > > Thanks in advance > > Maciekhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_= unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/se= nd_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.ne= t/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl= .net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl= .net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.sht= mlhttp://www.ccl.net/spammers.txt > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --20cf3054a2e9a366980495ccfe3e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Maciek,
I would try making a python, perl, or bash script that:
= 1) open the output file
2) search for the first line of the structure an= d step you're interested in (or a line with some "keyword" ne= xt to the beginning of the structure)
3) read the structure line by line counting the atom number in a variable a= nd when the "****" appears change them by the following variable = number i.e. 10000 and so on writing each line to a log/output file

In python, step 3 would by something like this:

n_at=3D 15000 #total= number of atoms of your structure
i=3D1
while i<=3Dn_at:
=C2= =A0 line=3Dfile_in.readline()
=C2=A0 subline=3Dline.split()
=C2=A0 if= i<9999:
=C2=A0=C2=A0=C2=A0 file_out.write(line)
=C2=A0 else:
=C2=A0=C2=A0=C2=A0 subline[0]=3Dstr(i)
=C2=A0=C2=A0=C2= =A0 file_out.write("%s "*len(subline)%tuple(subline))
=C2=A0 i= =3Di+1


(NOTE: please, check spelling and identation)


= Best

Esteban G Vega-Hissi
UNSL Argentina

--
2010/11/24 Close, David M. CLOSED{=3D}= mail.etsu.edu <owner-chemistry:ccl.net>

Sent to CCL by: "Close, David M." [CLOSED*mail.etsu.edu]
Maciej:
=C2=A0That's easy. =C2=A0One can purchase a program that is alre= ady compiled for a specific operating system. =C2=A0If you look at the Gaus= sian homepage you can select LINUX, WINDOWS, and a variety of parallel vers= ions. =C2=A0These programs can be installed with simple instructions on spe= cific machines. =C2=A0These packages are called machine language binaries. = =C2=A0As such you cannot read the code.
=C2=A0The other option is to purchase the actual program code (as in Fortr= an). =C2=A0These programs have to be compiled (or converted into binary cod= e), and then installed on the computer. =C2=A0This option is for people who= are developing code, or who are impatient with the numerous bugs that are = in most programs.
=C2=A0Therefore my original suggestion to your problem was to look at the = Fortran code and find the line that prints the output. =C2=A0Most likely it= calls for the atom number to be printed in fixed 4 space field (I4), that = you could easily try to fix. =C2=A0As someone else pointed out, in another = subroutine that used this output, you could cause a new problem with this a= ltered format.
=C2=A0Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu[a]ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu[a]ccl= .net] On Behalf Of MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es
Sent: Wednesday, November 24, 2010 4:21 AM
To: Close, David M.
Subject: CCL:G: ODP: CCL:G: Gaussia= n output problem


Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es]
Thanks for help but I'm completely begginer in gaussian and also in lin= ux so can you guys explain this thing with source code more precisely, plea= se?

Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing = stars to numbers manually :)

regards

Maciek
________________________________________
Od: owner-chemistry+maciejmarcin.maslyk=3D=3Dceu.es-x-ccl.net [owner-chemistry+maciejmarcin.= maslyk=3D=3Dceu.es-x-= ccl.net] w imieniu Abrash, Sam sabrash:_:richmond.edu [owner-chemistry-x-ccl.net]
Wys=C5=82ano: 23 listopada 2010 19:09
Do: MASLYK, MACIEJ MARCIN
Temat: CCL:G: Gaussian output problem

Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu]
Hi,

I think David is correct. =C2=A0However, there's a relatively easy fix = (I think) unless your atom count exceeds 9999 by a lot. =C2=A0Just go into = the output file with an editor, and replace the **** by the actual atom num= ber. =C2=A0That should fix the problem of not being able to read structures= (unless the program you're using for the structures has the same probl= em).

Sam

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone: =C2=A0804-289-8248
Fax: =C2=A0804-287-1897
E-mail: =C2=A0sabrash]|[r= ichmond.edu
Web-page: =C2=A0http://www.richmond.edu/~sabrash
"In 1893 Charles Hinton left Japan to become a mathematics instructor = at Princeton University, where he invented a baseball-pitching machine that= used gunpowder to propel the balls, like a cannon. =C2=A0After several acc= idents, the device was abandoned and Hinton lost his job ..." Terry Pr= atchett, Ian Steward and Jack Cohen, The Science of Diskworld III


-----Original Message-----
> From: owner-chemistry+sabrash=3D=3Drichmond.edu]|[ccl.net [mailto:owner-= chemistry+sabrash=3D=3Drichmond.edu]|[ccl.net] On Behalf Of Close, David M. CLOSED _ mail.etsu.edu
Sent: Tuesday, November 23, 2010 11:18 AM
To: Abrash, Sam
Subject: CCL:G: Gaussian output problem


Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu]
Maciej:
=C2=A0Do you own the source code? =C2=A0If so, look at the print command. = =C2=A0The program is most likely trying to print a 5 digit number in a fix = field (something like I4). =C2=A0Much of Gaussian code is in Fortran with f= ixed formats. =C2=A0The **** just mean that you have tried to print somethi= ng that doesn't fix in the space allowed.
=C2=A0Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu__ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu__ccl.net] On Behalf Of Maciej Ma= slyk maciejmarcin.maslyk .. ceu= .es
Sent: Tuesday, November 23, 2010 8:45 AM
To: Close, David M.
Subject: CCL:G: Gaussian output problem


Sent to CCL by: "Maciej =C2=A0Maslyk" [maciejmarcin.maslyk-,-ceu.es]
Hi everyone,
could you help me with one problem, please? Every time I'm running G03 = job I got problem with outputs. The problem is that I cannot extract struct= ures because there are stars **** instead of atom numbers higher than 9999.= Have you ever had this problem in your calculation if you had more than 99= 99 atoms in the system?

It looks like this in output:
=C2=A09995 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0-12.655571 =C2=A0 46.600810 =C2=A0 32.540627
=C2=A09996 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0-12.533484 =C2=A0 47.134581 =C2=A0 33.952118
=C2=A09997 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A08 =C2=A0 =C2=A0 =C2=A020001021= =C2=A0 =C2=A0 =C2=A0 =C2=A02.441067 =C2=A0-19.529269 =C2=A0 31.331119
=C2=A09998 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0 =C2=A02.813824 =C2=A0-19.307495 =C2=A0 32.184450
=C2=A09999 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0 =C2=A01.933916 =C2=A0-20.325103 =C2=A0 31.491166
=C2=A0**** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A08 =C2=A0 =C2=A0 =C2=A020001021= =C2=A0 =C2=A0 =C2=A0 37.587292 =C2=A0-11.572024 =C2=A0 28.812192
=C2=A0**** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0 37.333847 =C2=A0-11.927328 =C2=A0 27.960694
=C2=A0**** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0 38.095189 =C2=A0-12.272395 =C2=A0 29.221488
=C2=A0**** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A08 =C2=A0 =C2=A0 =C2=A020001021= =C2=A0 =C2=A0 =C2=A0 23.735956 =C2=A0-43.072924 =C2=A0 13.135294
=C2=A0**** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0 23.388276 =C2=A0-42.182008 =C2=A0 13.115359
=C2=A0**** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01 =C2=A0 =C2=A0 =C2=A020001030= =C2=A0 =C2=A0 =C2=A0 22.974070 =C2=A0-43.624340 =C2=A0 13.312930

Do you have any suggestions?

Thanks in advance

Maciekhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.n= et/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml=http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= agehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.= txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemis= try/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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--20cf3054a2e9a366980495ccfe3e-- From owner-chemistry@ccl.net Wed Nov 24 10:14:00 2010 From: "Michel Petitjean petitjean.chiral%x%gmail.com" To: CCL Subject: CCL: multiple conformations analysis free\open source\academic free software Message-Id: <-43214-101124100732-30866-slb1eHxcP5Gleo4bsz58YA[#]server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 Nov 2010 16:07:24 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral^gmail.com] Dear Andrew, Please have a look at the DIVCF freeware: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF Best regards, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral(!)gmail.com, michel.petitjean(!)univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2010/11/24 Andrew Voronkov drugdesign||yandex.ru : > > Sent to CCL by: Andrew Voronkov [drugdesign[]yandex.ru] > Dear CCL users, I have the next goal - to study multiple conformations of the compounds and  check the correlation with the biological activity. I'd like to cluster let's say top 50 conformations and divide them into similarity clusters as well as get representative and\or average structures for each of the clusters. > Is there any software which can help me with this? The conformations were generated using Frog2 server. > > > Best regards, > Andrew > From owner-chemistry@ccl.net Wed Nov 24 11:46:00 2010 From: "FyD fyd%%q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43215-101124113229-24546-gNptjfO0p7SLTJECOEeF/Q a server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 24 Nov 2010 17:31:53 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd()q4md-forcefieldtools.org] Dear Maciek, I do not think **** is a bug; simply in the format you have the room for only 4 characters... We encountered the same "problem" (not really one) in the Gaussian outputs related to molecular electrostatic potential computation. Using Perl, R.E.D. http://q4md-forcefieldtools.org/RED/ (you can download the code it is under the GNU General Public License) handles that easily using the code below (the code handles $NM molecules; $NC conformation & $w reorientations) - we first calculate the number of MEP points to define the max. number of points if(/ESP FIT Center/ig){ $nbpoint[$NM]++;} - then using this max. number of points you can do whatever you need; either save in another file with another format or re-build another Gaussian output... I am sure you could follow the same idea: you simply need to find the correct filter... regards, Francois for($NC=1;$NC <=$nbconf[$NM];$NC++){ for($w=1;$w<=$nbmod[$NM];$w++){ $nbpoint[$NM]=0; open(JOB2LOG,"){ if(/ESP FIT Center/ig){ $nbpoint[$NM]++;} } close(JOB2LOG); format_name ESPO "HEADER"; open(ESPO,">espot_m$NM-$NC-$w"); write ESPO; $flag1=$flag2=$i=0; open(JOB2LOG,"){ if((/Electrostatic Properties /ig)&&(/Atomic Units/ig)){ $flag1=1; } if($flag1 == 1){ $flag2++; } if(($flag2 > $nbatoms[$NM]+6)&&($flag2 < $nbpoint[$NM]+$nbatoms[$NM]+7)){ ($charge[$i][$NM])=(split(' '))[2]; $i++; } } close(JOB2LOG); $i=0; open(JOB2LOG,"){ if(/^ Atomic Center/ig) { ($x,$y,$z) = unpack("x32 A10 A10 A10",$_); $x=$x/0.529177249; $y=$y/0.529177249; $z=$z/0.529177249; printf ESPO (" %16.7E%16.7E%16.7E\n",$x,$y,$z); } if(/^ ESP Fit Center/ig) { ($x,$y,$z) = unpack("x32 A10 A10 A10",$_); $x=$x/0.529177249; $y=$y/0.529177249; $z=$z/0.529177249; printf ESPO ("%16.7E%16.7E%16.7E%16.7E\n",$charge[$i][$NM],$x,$y,$z); $i++; } } close(JOB2LOG); close(ESPO); } } > could you help me with one problem, please? Every time I'm running > G03 job I got problem with outputs. The problem is that I cannot > extract structures because there are stars **** instead of atom > numbers higher than 9999. Have you ever had this problem in your > calculation if you had more than 9999 atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? > Thanks in advance From owner-chemistry@ccl.net Wed Nov 24 15:32:00 2010 From: "Jamin Krinsky krinsky.jamin%gmail.com" To: CCL Subject: CCL:G: Gaussian 09 - Problems with TDDFT geometry optimization Message-Id: <-43216-101124152828-4850-/XpCIFhiSbd64I78zd8lHw{=}server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 Nov 2010 12:28:20 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin#,#gmail.com] Dear Ernst, Nobody has replied to this so I'll give it an educated guess. It could be something about specifying what is actually two-part job, the "opt freq" keyword combination. Gaussian must do numerical frequencies for TD jobs and maybe the keywords generated automatically for the second (frequency) part are not compatible with that method. I would do the two parts separately anytime the first part works and the second doesn't. You already have the optimization part done, so make a copy of the .chk file from that job with a new name (newfile.chk for example below) and make a new input like this: %nprocshared=8 %mem=4GB %chk=newfile.chk # freq td=(singlets,nstates=6,root=1) hf/6-31g(d,p) geom=checkpoint guess=read frequency part of calc 0 1 {make sure to put a few blank lines here!!!} You could also include the "read" option in the TD keyword to save some time but I can't remember exactly how that ends up behaving in these kinds of jobs. Regards, Jamin On Mon, Nov 22, 2010 at 4:42 AM, Ernst Horkel ehorkel++ioc.tuwien.ac.at wrote: > > Sent to CCL by: "Ernst  Horkel" [ehorkel=-=ioc.tuwien.ac.at] > Dear all, > > I intend to simulate electronic spectra of organic compunds using TDDFT level of theory. For this purpose I want to perform a geometry optimization of the 1st excited state (of benzene as an example) and an vibrational analysis of the minimum found. Unfortunately, the job fails and I have no idea why. IMHO the first job (geometry optimization) succeeds, but the second one doesn't. > > I am using G09 on a 8 core Opteron machine (all 8 cores, 4 GB RAM) > > So this is the (partial) output: > > -----SNIP------- > >   D24       -0.00016   0.00000   0.00000   0.00007   0.00007  -0.00009 >         Item               Value     Threshold  Converged? >  Maximum Force            0.000048     0.000450     YES >  RMS     Force            0.000017     0.000300     YES >  Maximum Displacement     0.000107     0.001800     YES >  RMS     Displacement     0.000032     0.001200     YES >  Predicted change in Energy=-1.673574D-08 >  Optimization completed. >    -- Stationary point found. >                           ---------------------------- >                           !   Optimized Parameters   ! >                           ! (Angstroms and Degrees)  ! >  --------------------------                            -------------------------- >  ! Name  Definition              Value          Derivative Info.                ! >  -------------------------------------------------------------------------------- >  ! R1    R(1,2)                  1.4138         -DE/DX =    0.0                 ! > > -----SNAP----- > > so this seems to tell me geometry optimization is OK; > > -----SNIP------- > > ZZZY=              0.0003 XXYY=            -89.8781 XXZZ=            -63.1837 YYZZ=            -63.1836 >  XXYZ=             -0.0003 YYXZ=             -0.0010 ZZXY=              0.0000 >  N-N= 2.014646440196D+02 E-N=-9.396066542997D+02  KE= 2.300858570874D+02 >  1\1\GINC-MASTER\FOpt\RTD-HF-FC\6-31G(d,p)\C6H6\HANMIK\22-Nov-2010\0\\# >  opt freq td=(singlets,nstates=6,root=1) hf/6-31g(d,p) geom=connectivi >  ty\\benzol-test tddft\\0,1\C,6.5168316274,1.2693566194,0.001738384\C,7 >  .9306171845,1.2692925681,0.0021804376\C,8.637562195,2.4936128114,0.001 >  6217232\C,7.930730751,3.7180250171,0.0006395457\C,6.5169664187,3.71808 >  94956,0.0001753444\C,5.8100105637,2.4937526246,0.000783884\H,5.9799138 >  434,0.3394581721,0.0021016335\H,8.467444507,0.3393399532,0.0029641075\ >  H,9.7113385438,2.4935793196,0.0019875469\H,8.4676875942,4.6479015869,0 >  .0002526738\H,5.980104819,4.6480239866,-0.0007186233\H,4.7362355123,2. >  4938321253,0.0004983426\\Version=AM64L-G09RevA.02\State=1-A\HF=-230.70 >  92354\RMSD=2.128e-09\RMSF=3.164e-05\Dipole=0.0000005,0.,-0.0000154\PG= >  C01 [X(C6H6)]\\_._ > > >  The arm of the moral universe is long, but it bends toward justice. >  -- Martin Luther King, Jr. >  Job cpu time:  0 days  0 hours 12 minutes  2.7 seconds. >  File lengths (MBytes):  RWF=     47 Int=      0 D2E=      0 Chk=      5 Scr=      1 >  Normal termination of Gaussian 09 at Mon Nov 22 13:16:17 2010. >  Link1:  Proceeding to internal job step number  2. >  ---------------------------------------------------------------------- >  #N Geom=AllCheck Guess=TCheck SCRF=Check GenChk RTD-HF(FC)/6-31G(d,p) >  Freq >  ---------------------------------------------------------------------- >  QPErr --- A syntax error was detected in the input line. >  Check SCRF=Check GenChk RTD-HF(FC)/6-31G >                               ' >  Last state="GCL" >  TCursr= 1046 LCursr=   54 >  Error termination via Lnk1e in /opt/g09/l1.exe at Mon Nov 22 13:16:17 2010. >  Job cpu time:  0 days  0 hours  0 minutes  0.2 seconds. >  File lengths (MBytes):  RWF=     47 Int=      0 D2E=      0 Chk=      5 Scr=      1 > > ------SNAP------- > > This are the last lines of the log file; This tells me there is a syntax error, which I do not understand... > > Here is the (complete) input: > > > %nprocshared=8 > %mem=4GB > %chk=benzene_tddft.chk > # opt freq td=(singlets,nstates=6,root=1) hf/6-31g(d,p) geom=connectivity > > benzol-test tddft > > 0 1 >  C                  6.52617188    1.28567244    0.00167800 >  C                  7.92133188    1.28567244    0.00167800 >  C                  8.61886988    2.49342344    0.00167800 >  C                  7.92121588    3.70193244    0.00047900 >  C                  6.52639088    3.70185444    0.00000000 >  C                  5.82878988    2.49364844    0.00099600 >  H                  5.97641288    0.33335544    0.00212800 >  H                  8.47083988    0.33315944    0.00299300 >  H                  9.71854988    2.49350344    0.00231200 >  H                  8.47141588    4.65407544    0.00042000 >  H                  5.97626888    4.65413544   -0.00095300 >  H                  4.72918588    2.49383144    0.00081600 > >  1 2 1.5 6 1.5 7 1.0 >  2 3 1.5 8 1.0 >  3 4 1.5 9 1.0 >  4 5 1.5 10 1.0 >  5 6 1.5 11 1.0 >  6 12 1.0 >  7 >  8 >  9 >  10 >  11 >  12 > > Btw, the input was generated using GaussView 5.0; so it should be OK? > > So my questions are: > > 1.) is it possible to perform the job in the way I intend to? > 2.) is the input correct? > 3.) what else can be wrong? > > Any ideas or hints are really welcome. > > Thank you in advance, > > Ernst Horkel, > > ehorkel_._ioc.tuwien.ac.at>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Nov 24 19:01:01 2010 From: "Computational Chemist computationalchemist[a]ymail.com" To: CCL Subject: CCL: charmm topology file Message-Id: <-43217-101124174026-3049-JNfsBtS0GKXNRP8Fscb4Qg]|[server.ccl.net> X-Original-From: Computational Chemist Content-Type: multipart/alternative; boundary="0-581847795-1290638420=:35160" Date: Wed, 24 Nov 2010 14:40:20 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Computational Chemist [computationalchemist.:.ymail.com] --0-581847795-1290638420=:35160 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi CCL, =A0 Is there any automated procedure to construct a a charmm topology file for = a new ligand? =A0 Thank you=0A=0A=0A --0-581847795-1290638420=:35160 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi CCL,
 
Is there any automated procedure to construct a a charmm topology file= for a new ligand?
 
Thank you

=0A=0A --0-581847795-1290638420=:35160-- From owner-chemistry@ccl.net Wed Nov 24 19:36:00 2010 From: "Anna Kuzak a.kuzak ~~ fqs.pl" To: CCL Subject: CCL: Special offer for Molecular Modeling Software - SCIGRESS 2.2 Message-Id: <-43218-101124104845-15705-gKt+0WZk73VhCp15rPCSNw{}server.ccl.net> X-Original-From: Anna Kuzak Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 24 Nov 2010 16:48:34 +0100 MIME-Version: 1.0 Sent to CCL by: Anna Kuzak [a.kuzak : fqs.pl] Dear All , FQS Poland (Fujitsu Group) is glad to announce a special, end of the year offer for molecular modelling software - SCIGRESS 2.2. The offer is valid till January 31, 2011. For details regarding the promotional pricing and discounts please contact us at ccs!=!fqs.pl. We offer both node-locked and floating licenses. For educational purposes we propose the Annual Academic Site Licenses option. SCIGRESS has been designed as a modular product to allow each user to choose only the components needed. SCIGRESS allows the user to apply a wide range of computational models, from molecular mechanics through rigorous quantum electronic structure techniques, to all types of molecular systems, from organic molecules, to inorganics, polymers, materials systems (metals, oxides, ceramics, semiconductors), and whole proteins. The computational power may be extended by optional multi-core compute engines for Windows and Linux. SCIGRESS is a successor of Scigress Explorer (CAChe) and Materials Explorer and integrates both programs into one powerful suite. SCIGRESS also offers interfaces to third party products allowing the user to combine all advantages under one comfortable graphical interface. If you require any further information or assistance from our side, please let us know. You may also vist: http://www.fqs.pl/Chemistry_Materials_Life_Science/products/scigress Best regards, Anna FQS Poland Sp. z o.o. (Fujitsu Group), e-mail: ccs!=!fqs.pl, tel: (+48) 12 429 43 45, fax: (+48) 12 429 61 24 From owner-chemistry@ccl.net Wed Nov 24 20:11:00 2010 From: "Olli Lehtonen olehtone]~[chem.helsinki.fi" To: CCL Subject: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43219-101124071231-2909-MbJrsGFgjxPaFZAWhNP/6w=-=server.ccl.net> X-Original-From: Olli Lehtonen Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 24 Nov 2010 14:12:22 +0200 MIME-Version: 1.0 Sent to CCL by: Olli Lehtonen [olehtone . chem.helsinki.fi] Hi, Apparently you are using linux so with scripting language awk you can write BEGIN {atom=10000} { if (/^\ \*\*\*\*/) { sub("^\\ \\*\\*\\*\\*",atom); atom++; } print $0; } Assuming that script is contained in file called stars.awk you then give a command (output follows) awk -f stars.awk test.out 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 10000 8 20001021 37.587292 -11.572024 28.812192 10001 1 20001030 37.333847 -11.927328 27.960694 10002 1 20001030 38.095189 -12.272395 29.221488 10003 8 20001021 23.735956 -43.072924 13.135294 10004 1 20001030 23.388276 -42.182008 13.115359 10005 1 20001030 22.974070 -43.624340 13.312930 where test.out contains your sample output. Just be aware that the script changes all **** (in the beginning of line with one extra space) with the running number so if you have the same problem someplace else in the output file it will change it there too. Hope it helps, Olli Oe Wed, Nov 24, 2010 at 10:20:47AM +0100, MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es wrote: > > Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] > Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? > > Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) > > regards > > Maciek > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es > Sent: Tuesday, November 23, 2010 8:45 AM > To: Close, David M. > Subject: CCL:G: Gaussian output problem > > > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > Hi everyone, > could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? > > Thanks in advance From owner-chemistry@ccl.net Wed Nov 24 20:46:00 2010 From: "Gegham Galstyan gegham * chemie.fu-berlin.de" To: CCL Subject: CCL: Question on calculation of charge center of electrons in a molecule Message-Id: <-43220-101124125216-32237-OBtMms360IT1noGRDqvxNw[]server.ccl.net> X-Original-From: "Gegham Galstyan" Date: Wed, 24 Nov 2010 12:52:14 -0500 Sent to CCL by: "Gegham Galstyan" [gegham^_^chemie.fu-berlin.de] Dear CCLers, I need to calculate the charge center of electrons in a small organic molecule. Is there any program that is able to do that? Many thanks beforehand. Best wishes, Gegham Galstyan Free University Berlin Institut fr Chemie und Biochemie Fabeckstrae 36a 14195 Berlin mailto: gegham(0)chemie.fu-berlin.de From owner-chemistry@ccl.net Wed Nov 24 21:21:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler+/-nhlbi.nih.gov" To: CCL Subject: CCL: charmm topology file Message-Id: <-43221-101124205526-4482-0TPh7aCun2NxYKmI5//6Yg#%#server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 Nov 2010 20:50:39 -0500 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#nhlbi.nih.gov] Not an official one (yet); I suggest browsing and searching the Parameter Set forum at www.charmm.org There's info there about the CHARMM General Force Field (CGenFF), and other tidbits about adding new molecules. ________________________________________ Sent: Wednesday, November 24, 2010 5:40 PM Subject: CCL: charmm topology file Hi CCL, Is there any automated procedure to construct a a charmm topology file for a new ligand? Thank you