Dear all I've used PyMol with the APBS plugin successfully with other structures but now it's giving problems with a model structure (made with Rosetta then SCWRL).
I set up the grid and then press run and the plug-in zips around the structure making a pqr file. However, I get an error message saying that some atoms are unassigned and that I should either delete them and restart the calculation or fix the parameters in the pqr file and use the modified version directly. Looking at the unassigned atoms, it seems to be standard protein - there is no exotic cofactor causing trouble. For example, here is one residue as loaded into PyMol 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 .... and here is the corresponding bit of the pqr file for one unassigned residue ATOM 2333 N TRP 157 -19.981 10.079 -4.038 0.000 0.000 ATOM 2334 C TRP 157 -21.189 10.376 -3.276 0.000 0.000 ATOM 2335 C TRP 157 -20.891 11.323 -2.118 0.000 0.000 ATOM 2336 O TRP 157 -21.507 11.233 -1.056 0.000 0.000 ATOM 2337 C TRP 157 -21.787 9.092 -2.697 0.000 0.000 ATOM 2338 C TRP 157 -20.856 8.356 -1.783 0.000 0.000 ATOM 2339 C TRP 157 -19.931 7.417 -2.137 0.000 0.000 It doesn't seem to make any difference if I add hydrogen with PyMol before trying to run the apbs plug-in. It's not a particular residue type that's problematic - I see Val, Cys, Glu, Thr, Phe etc also among the unassigned set. Can anyone help? Thanks very much Daniel -- 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.
