From owner-chemistry@ccl.net Sat Sep 3 04:25:33 2005 From: "CCL" To: CCL Subject: CCL: W:Could you help me to find the reason why my program does not work? Message-Id: <-29059-050903042349-20391-j6jGbi4IRXakbS2fcikGlA(-)server.ccl.net> X-Original-From: "Hua Ma" Sent to CCL by: "Hua Ma" [g0403132(-)nus.edu.sg] %chk=Rh-group.chk %mem=60MW OPT MP3/GEN Rh-group ......(molecular description) C H O 0 6-31G** **** Rh 0 LANL2DZ **** The program does not work successfully, but I do not know the reason. Best Regards, Ma Hua From owner-chemistry@ccl.net Sat Sep 3 08:20:40 2005 From: "CCL" To: CCL Subject: CCL: W:Could you help me to find the reason why my program does not work? Message-Id: <-29060-050903081851-18093-j6jGbi4IRXakbS2fcikGlA*_*server.ccl.net> X-Original-From: "XunLei Ding" Content-Type: text/plain Date: Sat, 03 Sep 2005 19:27:10 +0800 Sent to CCL by: "XunLei Ding" [dxl*_*ustc.edu.cn] You may try this: #OPT MP3/GENecp .... C H O 0 6-31G** **** Rh 0 LANL2DZ **** Rh 0 LANL2DZ In your mail: >From: "CCL" >Reply-To: "CCL Subscribers" >To: "Xunlei, Ding " >Subject: CCL: W:Could you help me to find the reason why my program does not work? >Date:Sat, 3 Sep 2005 04:37:25 -0400 > > > Sent to CCL by: "Hua Ma" [g0403132(-)nus.edu.sg] > %chk=Rh-group.chk > %mem=60MW > > OPT MP3/GEN > > Rh-group > > .....(molecular description) > > C H O 0 > 6-31G** > **** > Rh 0 > LANL2DZ > **** > > The program does not work successfully, but I do not know the reason. > > Best Regards, > Ma Hua> > > > From owner-chemistry@ccl.net Sat Sep 3 10:19:25 2005 From: "CCL" To: CCL Subject: CCL: W:Could you help me to find the reason why my program does not work? Message-Id: <-29063-050903063613-1234-o80D67vVBtiLxWnyey+vTg#%#server.ccl.net> X-Original-From: Laurence Cuffe Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Sat, 03 Sep 2005 12:42:08 +0100 MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [Laurence.Cuffe#%#ucd.ie] ----- Original Message ----- From: CCL Date: Saturday, September 3, 2005 9:25 am Subject: CCL: W:Could you help me to find the reason why my program does not work? Shure! it would help if you can give us a copy of the end of the log file, as that makes working out whats going on a lot easier. All the best Dr Laurence Cuffe > > Sent to CCL by: "Hua Ma" [g0403132(-)nus.edu.sg] > %chk=Rh-group.chk > %mem=60MW > > OPT MP3/GEN > > Rh-group > > .....(molecular description) > > C H O 0 > 6-31G** > **** > Rh 0 > LANL2DZ > **** > > The program does not work successfully, but I do not know the reason. > > Best Regards, > Ma Hua > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST#%#ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Sat Sep 3 10:19:25 2005 From: "CCL" To: CCL Subject: CCL: Automated standardization of atom names in PDB? Message-Id: <-29061-050903100758-7630-o80D67vVBtiLxWnyey+vTg---server.ccl.net> X-Original-From: Nathan Baker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 03 Sep 2005 08:17:32 -0500 MIME-Version: 1.0 Sent to CCL by: Nathan Baker [baker---biochem.wustl.edu] You might try PDB2PQR: http://agave.wustl.edu/pdb2pqr. This will assign atom names, add missing atoms, etc. Good luck, Nathan CCL wrote: > Sent to CCL by: Dr Seth Olsen [s.olsen1*|*uq.edu.au] > > Hi CCLers, > > Does software exist that will take a PDB format file with non-standard > atom names and determine the standard atom labelling for the atoms in a > file (if the file contains a protein with regular amino acid residues)? > > I have a PDB file that was run through a chemistry utility, and in the > process the usual PDB labelling (i.e. CA, CB, HB etc.) was changed to a > much less informative format. The program also modified the structure > in such a way that pasting the old names in to the appropriate field is > not feasible. To check all atoms would be time-consuming, but since > most amino acids in the protein are unmodified, the correct atom > labelling should be clear from the bond topology. Is there a program > that will read the topology and determine the standard atom names? > > Cheers, > > Seth > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group > Centre for Computational Molecular Science > Chemistry Building, > The University of Queensland > Qld 4072, Brisbane, Australia > > tel (617) 33653732 > fax (617) 33654623 > email: s.olsen1---uq.edu.au > Web: www.ccms.uq.edu.au > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms> > -- Nathan Baker, Assistant Professor Washington Univ., Dept. of Biochemistry and Molecular Biophysics From owner-chemistry@ccl.net Sat Sep 3 10:19:25 2005 From: "CCL" To: CCL Subject: CCL: W:Symmetry "Gaussian" Message-Id: <-29062-050903041628-19900-o80D67vVBtiLxWnyey+vTg_-_server.ccl.net> X-Original-From: "Ali Salimi" Sent to CCL by: "Ali Salimi" [salimi_ali2002_-_yahoo.com] Dear CCLers I am student. I use G98 for calculations. I have a problem about symmetry of my strucutre. D3d point group must be for my calculations because I want to obtain normal mode for my compound. But C2h point group has been done in my caculation. I want to know, How do I D3d symmetry for my compound. I use XYZ for input file. Thanks a lot for your attentions. Your sincerely A. Salimi E-mail:salimi_ali2002_-_yahoo.com From owner-chemistry@ccl.net Sat Sep 3 10:38:32 2005 From: "CCL" To: CCL Subject: CCL: Molpro and gmainv1 failure Message-Id: <-29064-050903102516-24191-o80D67vVBtiLxWnyey+vTg]"[server.ccl.net> X-Original-From: Alexander Martins Silva Content-Type: multipart/alternative; boundary="------------040709050507060906080409" Date: Sat, 03 Sep 2005 10:31:59 -0300 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva]"[uol.com.br] This is a multi-part message in MIME format. --------------040709050507060906080409 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi all, I have a linux machine with 4GB of memory and I'm trying to execute a job with this memory limit but I can't. The error message is the following: Failure in attempting memory allocation of 180230002 words (1375 Mbyte) This error has been generated by the operating system, and may be the result of insufficient system memory or paging space In order to avoid the problem in the MOLPRO context, consider also reducing the requested memory through the MEMORY input command, or the -m command line option gmainv1 failure to allocate 180230002 I already had done a small search for similar issues and I had found that a possible problem is the datasize and stacksize limits, but the problem stills even after changing these values to unlimited: #ulimit -acore file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited file size (blocks, -f) unlimited max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 7168 virtual memory (kbytes, -v) unlimited How can I solve this problem? Thanks, Alexander. --------------040709050507060906080409 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
          Hi all,

          I have a linux machine with 4GB of memory and I'm trying to execute a job with this memory limit but I can't.  The error message is the following:

Failure in attempting memory allocation of 180230002 words (1375 Mbyte)
This error has been generated by the operating system,
and may be the result of insufficient system memory or paging space
In order to avoid the problem in the MOLPRO context,
consider also reducing the requested memory through
the MEMORY input command, or the -m command line option
gmainv1 failure to allocate 180230002

            I already had done a small search for similar issues and I had found that a possible problem is the datasize and stacksize limits, but the problem stills even after changing these values to unlimited:
#ulimit -acore file size        (blocks, -c) 0
data seg size         (kbytes, -d) unlimited
file size             (blocks, -f) unlimited
max locked memory     (kbytes, -l) unlimited
max memory size       (kbytes, -m) unlimited
open files                    (-n) 1024
pipe size          (512 bytes, -p) 8
stack size            (kbytes, -s) unlimited
cpu time             (seconds, -t) unlimited
max user processes            (-u) 7168
virtual memory        (kbytes, -v) unlimited

       How can I solve this problem?

                Thanks,

                         Alexander.
         
--------------040709050507060906080409-- From owner-chemistry@ccl.net Sat Sep 3 19:56:20 2005 From: "CCL" To: CCL Subject: CCL: QM with surrounding point charges, damping, etc. Message-Id: <-29065-050903104603-11912-o80D67vVBtiLxWnyey+vTg_+_server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sat, 3 Sep 2005 17:00:13 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson_+_helsinki.fi] Hello All! I've slowly started getting my foot (spoon?) into QM/MM, and the first step (spoonful) has been to look at a QM region surrounded by point charges. These point charges are supposed to represent the inhomogeneous field of a surrounding protein structure. The values for the point charges are taken either directly from a standard force field (e.g., AMBER, CHARMM) or are obtained from ESP fitted charges. Now for the newbie-asking-questions part, in two parts: 1.) Should the charges surrounding the QM region be damped distance dependently or not? What articles I have browsed don't really discuss this, and it seems to me it is usually _not_ done. In pure MM calculations, on the other hand, a damping factor (epsilon) is usually used and recommended for the long range interaction. The reason, screening, is also clear to me. Why is the situation when studying the interaction of a QM region with distant point charges different? Or is it? 2.) (Total) charge of the system and subsystems. Are there recommendations on what the overall charge in the (sub)systems should be? Is there, for example, any order of preference for the following situations: a) total charge of QM = pc = 0 (generally difficult to obtain) b) total charge of QM + pc = 0, with q(QC) = -q(pc) c) charge of QM any integer, q(pc) = 0 d) charge of QM any integer, q(pc) any real number e) insert better suggestion here :-) Of course, references / book recommendations / other sources of info on the generel subject are very welcome on top of wise advice! Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/