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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 > > Hi Haoxi, > > The detail of the implicit membrane setup can be found in the following paper: > > Journal of Chemical Theory and Computation 13 (7), 3398–3412, 2017 > > which addresses most of your questions. Briefly: > > 1. How can I find out the best position to put the membrane center (mctrdz) and the thickness (mthick)? > > This is discussed in detail in the paper. You'll need to measure the > membrane thickness and its center for each snapshot by manipulating > the membrane coordinates from your MD trajectory. Remember to first > image all atoms into the unit cell using cpptraj. Then compute the > average thickness and center for the trajectory and use it in mmpbsa. > > We will release a python script to facilitate the membrane setup in > the next release. > > 2. If the protein is just a receptor rather than ion channels, should I still set poretype=1? > > It's not necessary. > > 3. In the sample input file for MMPBSA with membrane proteins in Amber manual, bcopt was set to 10 and eneopt to 1. But under the detailed explanation of eneopt option, it was emphasized that eneopt=1 requires a nonzero CUTNB and BCOPT = 5. What value should I use for bcopt and eneopt respectively? > > You'll have to use BCOPT=10, the periodic boundary for membrane > proteins. BCOPT=5 is for water soluble proteins. ENEOPT=1 works for > both boundary conditions. > > 4. To run this calculation, I prepared 3 parameter/topology files (only complex, protein, ligand) and only kept protein and ligand in the MD trajectory. Is there any other files I need to make? In the MMPBSA tutorial on the website, the solvated parameter/topology file of the complex was also used via -sp option, but when I use it there was an error. Is it necessary to use the -sp option? > > There is no difference between membrane proteins and globular proteins > in this regard. Please study the mmpbsa tutorials first to understand > the basic procedure. > > 5. Here are the parameter settings that I’m planning to use. Can I ask for some suggestions? > > As for the keywords, please first use those in the mmpbsa test case > for the membrane proteins. Let's see what problem you still have after > addressing the above concerns. > > All the best, > Ray > -- > Ray Luo, Ph.D. > Professor of Structural Biology/Biochemistry/Biophysics, > Chemical and Materials Physics, Chemical and Biomolecular Engineering, > Biomedical Engineering, and Materials Science and Engineering > Department of Molecular Biology and Biochemistry > University of California, Irvine, CA 92697-3900 > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org<mailto:AMBER.ambermd.org> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SSRyv2p8U1S1O1OKefEt8WnSpJO5RS47PLTtN6Y14jU&m=iypT555cNdqfN3g6QVYCvIEXtPEPEDKvSxOsjIVvSgA&s=C36L6Gyx1I1K_hKLojwZi3SqBtkoSmI2vdROR1b2SSo&e= > > _______________________________________________ > 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 Thu Jun 18 2020 - 13:00:04 PDT