I got it. I have looked at the input files for the T4-lysozyme tutorial available at alchemistry.org. They have defined state A and state B. I am using GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual decoupling parameters are taken from the mdp options, like by defining [lambda-moltype] in mdp file. As I know from the tutorials and manual the solvation free energy of the ligand can calculated.
>From the alchemistry.org input files, the topology parameters of ligand are inserted in protein topology named as complex.top. If I follow the same protocol without defining the state B of the ligand in topology, how the ligand molecule will be decoulped in complex. On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 10:29 PM, tasneem kausar wrote: > >> Thank you for your reply >> >> In last section of your tutorial you have suggested some changes to made >> in >> mdp file. That can be used for solvation free energies. >> For free energy calculation of protein drug complex, is it only lambda >> restraint to be defined? >> >> > Along with a complex system of [intermolecular_interactions] that preserve > the relative orientation of the ligand. This is a very complex calculation > in practice. See examples on alchemistry.org and in the literature in > works by Roux, Im, Karplus, etc. My tutorial is not very useful for such > calculations; it is extremely basic relative to what is needed to carry out > a binding free energy calculation. I only mentioned it there because so > many people asked about it and I wanted to clear up any confusion. > > -Justin > > > On 8 Jan 2017 01:45, "Justin Lemkul" <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/7/17 6:05 AM, tasneem kausar wrote: >>> >>> Dear all >>>> >>>> I am following Justin's tutorial methane in water for free energy >>>> calculation. I am using Gromacs-5.1.4. The charges of methane in >>>> topology >>>> are set to zero. So following the same protocol, is it relevant to set >>>> the >>>> charges at zero in topology of the drug. I am confused because in >>>> tutorial >>>> of Sander (ethanol in water) charges are present in the topology file. >>>> >>>> Please tell me the difference in both the tutorials and how can I apply >>>> it >>>> to drug that I want to study. >>>> >>>> >>>> The charges in my tutorial are set to zero because the stated goal of >>> that >>> tutorial is to reproduce *only the LJ portion of the hydration free >>> energy* >>> to match a published paper. This creates a very simple, robust system. >>> If >>> you want to calculate a real, meaningful hydration or binding free >>> energy, >>> charge transformation is required. >>> >>> -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. >>> >>> > -- > ================================================== > > 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.