Dear Justin, During the pulling part of the umbrella sampling for finding binding affinity of the Protien-ligand system, the ligand(peptide) is deformed and its helices straighten along with large conformational changes in Protein. This is when the pull_coord1_dim = Y Y Y. But when I had used pull_coord1_dim = N N Y for one of the systems the peptide helices didn't deform. Is it reasonable for the ligand helices to deform when finding properties like Binding affinity?
Can it be avoided if the ligand orientation is not known and using pull_coord1_dim = Y Y Y is necessary. Best Regards, Bhagyesh ----- Original Message ----- From: "Varvdekar Bhagyesh Rajendra" <bhagyesh.varvde...@research.iiit.ac.in> To: gmx-us...@gromacs.org Sent: Wednesday, May 31, 2017 6:42:41 PM Subject: Re: [gmx-users] Doubt about gmx wham analysis Dear Justin, Many Thanks for the swift reply and the help in answering my doubts. Best Regards, Bhagyesh ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Wednesday, May 31, 2017 6:06:59 PM Subject: Re: [gmx-users] Doubt about gmx wham analysis On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the > ligand is pulled along the COM of two groups protein-ligand in all directions > to calculate binding affinity using umbrella sampling. On the other hand, the > tutorials use pull_coord1_dim = N N Y. Hence, I concluded my reaction > coordinate differs as mentioned in the help menu of gmx wham : "If you have > some unusual reaction coordinate you may also generate your own .pdo files > and feed them with the -ip option into to gmx wham" > The fact that your reaction coordinate is different from the tutorial is irrelevant. You have an absolutely normal reaction coordinate and does not apply to what the gmx wham help text is talking about (which is probably a very outdated note at this point, given the massive changes in the pull code in recent versions). > Also, the following warning is thrown by gmx wham: " WARNING, no data point > in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your > histograms! " > I was not sure if the z corresponds to the coordinate axis or just the z-axis > (which was not the only reaction coordinate in my system). > It is the length along zeta, the reaction coordinate. Don't confuse it with the z-axis, it's just shorthand. > All this made me conclude that the pullx files are not enough and the so > called pdo files must be necessary, hence the doubt arised. I would > appreciate if some more light is shed in this area. > You need better sampling, not archaic file formats. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
