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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Thu, Jun 5, 2014 at 4:25 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > Zahra, > > One reason for the reported failure is that the receptor has not a > single atom charged … the force driver simply skip the call to > pb_force() in this situation. This is probably too crude for you since > your nanotube was built with neutral atoms on purpose. This is not a > negligence. I'll supply an update to allow van der Waals calculation > to go through in this situation ... > > I'm trying to understand why the program complaints about the non > bonded list for the complex that does contains charged atoms … > > All the best, > Ray > -- > Ray Luo, Ph.D. > Professor, > Biochemistry, Molecular Biophysics, and > Biomedical Engineering > University of California, Irvine, CA 92697-3900 > > > On Wed, Jun 4, 2014 at 10:52 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: >> Zahra, >> >> Can you email me off the list your prmtop/inpcrd to take a look? There >> shouldn't be such error messages any more after our recent updates. >> >> Did you patch all updates and pass the tests for AmberTools 13? >> >> Ray >> >> On Jun 4, 2014 6:01 AM, "Jason Swails" <jason.swails.gmail.com> wrote: >>> >>> On Tue, 2014-06-03 at 13:17 -0700, zahra khatti wrote: >>> > AmberTools13 >>> >>> I'm not sure what the "correct" fix for this problem is. You can try >>> googling the error message, which will bring up previous threads that >>> may help you solve the problem. >>> >>> You can also try increasing the maxnba estimate in >>> $AMBERHOME/AmberTools/src/pbsa/pb_init.F90 (look at line 215) if none of >>> the suggestions from past email threads work. >>> >>> You can print out the value of eclose + pclose + sclose + nclose + cntr >>> as well as maxnba in pb_list.F90 (~line 699) to see how much bigger you >>> need to make maxnba. >>> >>> If none of these work, I'll have to defer to a PBSA developer. >>> >>> Good luck, >>> Jason >>> >>> -- >>> Jason M. Swails >>> BioMaPS, >>> Rutgers University >>> Postdoctoral Researcher >>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jun 20 2014 - 08:30:02 PDT