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.
