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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Mon, Mar 24, 2014 at 8:52 AM, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote: > What I don't understand is why does "cavity_offset" defaults to 0.000 > for inp=1 ? > From the original paper by Sitkoff et al 2004 (Barry Honig's group) it > should be 0.86 ... Or ? Am I missing something ? > > Vlad > > > On 03/24/2014 04:41 PM, Jason Swails wrote: >> On Mon, 2014-03-24 at 12:24 -0300, George Tzotzos wrote: >>> Hi Jason, >>> >>> I have had the same problem (i.e. GB energy of ligand binding (-)ve >>> and PB (+)ve. Setting inp=1, throws out the following warnings: >>> >>> Warning: inp=1 was old default >>> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to inp=1 default value: 0.0050 >>> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to inp=1 default value: 0.000 >>> >>> my mmpbsa input file is: >>> >>> Input file for running PB and GB >>> &general >>> >>> interval=2, endframe=2000, verbose=1, >>> # entropy=1, >>> / >>> &gb >>> igb=2, saltcon=0.100 >>> / >>> &pb >>> inp=1, istrng=0.100, >>> / >>> >>> Any explanation for this would be much appreciated. What other >>> settings are needed to overcome this problem? >> The inp=1 and inp=2 nonpolar solvation models are completely different. >> In my experience, the inp=2 model is more destabilizing than the inp=1 >> model (whether for better or worse, I don't know). The default >> parameters for the nonpolar solvation method differs depending on which >> model you're using, so the warning messages you see is just an >> indication that the default inp=2 parameters are being reset to the >> default inp=1 parameters (which is consistent with the results you used >> to get in previous versions of AmberTools with inp=1). >> >> Of course if you really wanted to compare apples to apples you could >> simply substitute the GB nonpolar solvation free energy contribution >> into the PB results and recompute your binding free energy that way. >> This is equivalent to "using the same nonpolar model" for both GB and >> PB. >> >> HTH, >> Jason >> > > -- > Dr. Vlad Cojocaru > Computational Structural Biology Laboratory > Department of Cell and Developmental Biology > Max Planck Institute for Molecular Biomedicine > Röntgenstrasse 20, 48149 Münster, Germany > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru > > > _______________________________________________ > 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 Mon Mar 24 2014 - 13:00:03 PDT