Bugs item #1639319, was opened at 2007-01-19 02:45 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1639319&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) >Assigned to: Bob Hanson (hansonr) Summary: reading nwchem output Initial Comment: I run an scf_simple_input job as described at 2.2 of the NWChem manual. For water I simply replaced the nitrogen coordinates with those for waters (from my MM packages), set correctly the basis, and all OK. As output, I added the ususl unix "| tee" to the command, getting the requested *.out file, which debian sees as a MOPAC-type file (attached). Question: how to read this file with Jmol 11 on debian i386 etch? As such it does not open with Jmol 11 and changing the extension has no meaning. Or did you plan that an ECCE output is first obtained (I never tried that)? I would prefer - for my current type of work - not to pass through ECCE. Ideally, for a NWChem "geometry optimization" Jmol should read all intermediate "molecules" and not only the finally-optimized one. This would afford a view on the whole minimization process. Sometimes it is useful, particularly when convergence is difficult to attain. Additional question: I read correctly with Jmol 11 a pdb file generated with my MM package. Though, only the heavy atoms could be numbered, not the hydrogens (while hydrogens are numbered by my MM application). If this was not my mistake, Jmol would not allow to read dihedrals with hydrogens, while these are the most common experimental evidence from 1H NMR spectra. Thank you for providing such a beautiful tool as Jmol. Attached are output file for both nitrogen and water. Thanks a lot for your kind attention francesco pietra PS: it seems that only one file can be attached, therefore I attached water ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2007-02-07 23:16 Message: Logged In: YES user_id=1082841 Originator: NO NWChem reader should be OK now in 11.1.9 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2007-02-04 13:21 Message: Logged In: YES user_id=1082841 Originator: NO Francesco -- could you please send me the PDB file? Bob Hanson [EMAIL PROTECTED] ps. We've just done some more modifications to the NWChem reader -- it was not properly parsing molecular orbitals and basis functions. Should be OK now in 11.0 and 11.1 ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2007-01-22 12:41 Message: Logged In: YES user_id=905185 Originator: NO I just committed some modifications to the NWChemReader.java that takes care of the exception thrown, so the enclosed file reads properly. I forgot to answer your question about ECCE: no, the reader reads the standard output created by NWChem. I am sorry that I can not address your question regarding the pdb file from your MM packages. Maybe somebody else can do that? Thanks, René ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2007-01-19 11:05 Message: Logged In: YES user_id=905185 Originator: NO I tried your file with the latest build of Jmol (where I had uploaded some changes in Jmol to be able to recognize nwchem files since the output between 4.7 and 5.0 changed a bit in the first lines) and your file is not read properly. When I run the same input you had (from section 2.2 in the manual), I can read the file fine, except that the colors for the atoms are not interpreted properly. I assume this is because of using n as opposed to N for the atoms. I did a diff between my run on the water example that you had uploaded and the only difference that could be problematic is the fact that in your version of nwchem the geometry output has after list of atoms not an empty line, but a line with a space in it.... I have to leave town this afternoon, so I don't have the time to fix it right now, but I am surprised that that kind of difference may occur between different compiles of nwchem (I am running on Mac OS X, so I compiled it myself). René ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1639319&group_id=23629 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
