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.
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.
On Tue, 2006-07-18 at 09:32 -0400, Peter Adrian Meyer wrote:
> 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,
> > 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.
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> 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
Liverpool L69 7ZB, U.K.