AMBER Archive (2009)

Subject: Re: [AMBER] problem of mm_pbsa

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Fri Aug 07 2009 - 20:11:43 CDT


Hi Jordan Monnet, † Thanks for your interest in this problem! The attached files are what you ask me to attach. Thanks! † Best wishes! † Qinghua Liao ________________________________ From: Jordan Monnet <monnet.jordan_at_free.fr> To: AMBER Mailing List <amber_at_ambermd.org> Sent: Saturday, August 8, 2009 7:13:57 AM Subject: Re: [AMBER] problem of mm_pbsa Hello, Can you send us one of your "something_com.all..out" from the run which gives you these weird results? --Jordan * Qinghua Liao (fantasticqhl_at_yahoo.com) wrote: > Hi sir, > Many thanks for your reply! I have done that too, but there is no problem. I am wondering that maybe the two structural waters will make a difference, so I am just doing another simulation without the two structural waters. Thanks! > > Best wishes! > > Qinghua Liao > > > > ________________________________ > From: Rubben Torella <rubben.torella_at_gmail.com> > To: AMBER Mailing List <amber_at_ambermd.org> > Sent: Thursday, August 6, 2009 11:53:47 PM > Subject: Re: [AMBER] problem of mm_pbsa > > Hi, > try to check the structures of the ligand, repector and complex you created > for the analysis... > use the ambpdb command and check if every structure is correct... > Hope this could help... > > 2009/8/5 case <case_at_biomaps.rutgers.edu> > > > On Tue, Aug 04, 2009, Qinghua Liao wrote: > > > > > I have a problem when I use mm_pbsa in amber 10¬ to calculate the > > > binding energy of the complex. After docking using autodock 4.0, I chose > > > a conformation of the ligand, which matched well with the crystal ligand > > > in the complex, to do MD with the receptor, two structural waters were > > > preserved. I got a sample of 4ns, a equilibrated system according to the > > > RMSD of the backbone. > > > > > > But the binding energy is abnormal: > > > > > > #† † † † † † † † † COMPLEX† † † † † † † † RECEPTOR > > LIGAND > > > #† † † † † ----------------------- ----------------------- > > ----------------------- > > > #† † † † † † † † † MEAN† † † † STD† † † † MEAN† † † † STD > > MEAN† † † † STD > > > #† † † † † ======================= ======================= > > ======================= > > > ELE† † † † † † -8427.58† † 249.82† † -7913.17† † 248.20 > > -504.26† † † 14.77 > > > VDW† † † † 21573827.80† 32502.03† 20373193.05† 31945..80 > > 1200511.78† † 3894.24 > > > INT† † † † † 7034641.54† 60631.76† 6982919.11† 60080.98 > > 51722.43† † 5624.52 > > > GAS† † † † 28600041.76† 67739.75† 27348198.98† 66677.44 > > 1251729.96† † 7136.00 > > > PBSUR† † † † † † 104.47† † † 1.36† † † 104.04† † † 1.33 > > 4.94† † † 0.08 > > > > You will have to do the analysis (at least some of it) "by hand".† Look at > > the > > output files from your simulation: why do you have such high van der Waals > > and > > internal energies? > > > > The MM-PBSA perl scripts are nice when everything works, but are much less > > helpful when problems show up.† In such circumstances, you should at least > > a > > part of the analysis yourself, so that you really understand what is being > > computed.† Further, everyone's "first" analysis should also be done this > > way. > > > > ....good luck...dac > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER_at_ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER_at_ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > >† > _______________________________________________ > AMBER mailing list > AMBER_at_ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber † † }><(({*> __/ Jordan MONNET Bachelor in Biology & Computer science University of Paris Diderot (Paris VII) http://monnet.jordan.free.fr/ _______________________________________________ AMBER mailing list AMBER_at_ambermd.org http://lists.ambermd.org/mailman/listinfo/amber









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