Dear all After following the suggestion to try apbs at the command line and some googling, I found that the problem was that new-ish apbs 0.4 was expecting a new keyword 'sdens' that my slightly old apbs plugin for PyMol was not outputting.
http://sourceforge.net/mailarchive/forum.php?thread_id=9502914&forum_id=46597 http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6140.html With the new version of apbs plugin this issue is resolved so can get it to work with *externally generated* pqr files. However, the self-made pqr files *still* come with the unassigned atom problem I mentioned before. Any help on that very welcome. Daniel On Tue, 2006-07-18 at 09:32 -0400, Peter Adrian Meyer wrote: > Hi, > > It's good to hear that you got things working, or are at least one step > closer. Other than the usual troubleshooting steps that you've probably > alread tried (checking to make sure that the file exists, path is correct, > running apbs from the command line to make sure it's happy, etc), I don't > have any other ideas. > > Good luck, > > Pete > > > Hi Pete > > > > Thanks for the idea. In fact adding a chain ID doesn't make any > > difference in this case. > > > > Based on a mail from Kostas Tripsianes I successfully used the pdb2pqr > > server to get a pqr file independently to feed to the plug-in. I got a > > good looking pqr file but when I try to run apbs, after setting the > > grid, I now get this error message > > > > ObjectMapLoadDXFile-Error: Unable to open file! > > > > Does anyone know why that is? > > > > Thanks again > > > > Daniel > > > > On Mon, 2006-07-17 at 14:51 -0400, Peter Adrian Meyer wrote: > >> Hi Daniel, > >> > >> Based on your atom lines, it looks like the pdb -> pqr conversion may > >> not > >> be happy about not having a chain ID in the pdb file (this might not be > >> the problem, but it's worth a shot). You could test this with a pdb > >> file > >> that has chain IDs, or assign them to the pdb file you're working with. > >> > >> > ATOM 1191 N TRP 157 -19.981 10.079 -4.038 1.00 0.00 > >> > ATOM 1192 CA TRP 157 -21.189 10.376 -3.276 1.00 0.00 > >> > ATOM 1193 C TRP 157 -20.891 11.323 -2.118 1.00 0.00 > >> > ATOM 1194 O TRP 157 -21.507 11.233 -1.056 1.00 0.00 > >> > ATOM 1195 CB TRP 157 -21.787 9.092 -2.697 1.00 0.00 > >> > ATOM 1196 CG TRP 157 -20.856 8.356 -1.783 1.00 0.00 > >> > ATOM 1197 CD1 TRP 157 -19.931 7.417 -2.137 1.00 0.00 > >> > >> If this doesn't resolve things, hopefully one of the apbs guru's will be > >> able to tell you what's going on. > >> > >> Pete > >> > >> > >> > >> Pete Meyer > >> Fu Lab > >> BMCB grad student > >> Cornell University > >> > > -- > > Dr Daniel John Rigden Tel:(+44) 151 795 4467 > > School of Biological Sciences FAX:(+44) 151 795 4406 > > Room 101, Biosciences Building > > University of Liverpool > > Crown St., > > Liverpool L69 7ZB, U.K. > > > > > > ------------------------------------------------------------------------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share > > your > > opinions on IT & business topics through brief surveys -- and earn cash > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > > PyMOL-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
