Thread: [Apbs-users] problem with apolar calculation with apbs 1.0.0
Biomolecular electrostatics software
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From: 龚. <gl...@ma...> - 2008-06-27 07:11:00
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Dear all, I met a problem when calculating apolar bind energy with apbs. The error message is, Reading PQR-format atom data from com.pqr. initAPOL: Got NULL Vparam object! Error calculating apolar solvation quantities! 26336 atoms Centered at (1.402e+00, 1.641e+00, -3.735e-01) Net charge -6.00e+01 e Preparing to run 3 PBE calculations. could you tell me what's wrong here. My input file is (the parameters are basically the same with the alkanes example) read mol pqr lig.pqr mol pqr rec.pqr mol pqr com.pqr end apolar name acom grid 0.3 0.3 0.3 mol 3 srfm sacc swin 0.3 srad 1.40 press 0.2394 gamma 0.0085 bconc 0.033428 sdens 100.0 dpos 0.2 temp 298.15 calcenergy total calcforce no end apolar name arec grid 0.3 0.3 0.3 mol 2 srfm sacc swin 0.3 srad 1.40 press 0.2394 gamma 0.0085 bconc 0.033428 sdens 100.0 dpos 0.2 temp 298.15 calcenergy total calcforce no end apolar name alig grid 0.3 0.3 0.3 mol 1 srfm sacc swin 0.3 srad 1.40 press 0.2394 gamma 0.0085 bconc 0.033428 sdens 100.0 dpos 0.2 temp 298.15 calcenergy total calcforce no end print energy acom - arec - alig end quit |
From: Nathan B. <sob...@gm...> - 2008-06-27 11:55:51
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Hello -- I'm sorry you received such a cryptic error -- we'll work to make this clearer in the future. APBS is complaining because you are performing an apolar calculation with the van der Waals integral term. This term requires van der Waals parameters which are not available from the PQR file. Therefore, you need to supply a parameter file with the keyword read parm flat amber94.dat end (for example), where the relevant parameter files can be found in apbs/ tools/conversion/param/vparam. I hope this helps. -- Nathan On Jun 27, 2008, at 2:10 AM, 龚麟宸 wrote: > Dear all, > > I met a problem when calculating apolar bind energy with apbs. > The error message is, > > Reading PQR-format atom data from com.pqr. > initAPOL: Got NULL Vparam object! > Error calculating apolar solvation quantities! > 26336 atoms > Centered at (1.402e+00, 1.641e+00, -3.735e-01) > Net charge -6.00e+01 e > Preparing to run 3 PBE calculations. > > could you tell me what's wrong here. > > My input file is (the parameters are basically the same with the > alkanes example) > > read > mol pqr lig.pqr > mol pqr rec.pqr > mol pqr com.pqr > end > > apolar name acom > grid 0.3 0.3 0.3 > mol 3 > srfm sacc > swin 0.3 > srad 1.40 > press 0.2394 > gamma 0.0085 > bconc 0.033428 > sdens 100.0 > dpos 0.2 > temp 298.15 > calcenergy total > calcforce no > end > > apolar name arec > grid 0.3 0.3 0.3 > mol 2 > srfm sacc > swin 0.3 > srad 1.40 > press 0.2394 > gamma 0.0085 > bconc 0.033428 > sdens 100.0 > dpos 0.2 > temp 298.15 > calcenergy total > calcforce no > end > > apolar name alig > grid 0.3 0.3 0.3 > mol 1 > srfm sacc > swin 0.3 > srad 1.40 > press 0.2394 > gamma 0.0085 > bconc 0.033428 > sdens 100.0 > dpos 0.2 > temp 298.15 > calcenergy total > calcforce no > end > > print energy acom - arec - alig end > > quit > > > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php_______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |