So there is! Many thanks for bringing this to my attention.
Thanks Anthony On 29/05/2016 20:40, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of jalem...@vt.edu> wrote: > > >On 5/29/16 3:37 PM, Nash, Anthony wrote: >> Dear all, >> >> I¹m a total newbie when it comes to Thermodynamic Integration, and until >> now I¹ve been happy with umbrella sampling. However, I¹ve found myself >>in >> a situation where I believe TI would be the most appropriate technique. >> >> I would like to determine the energetic contribution that a mutant amino >> acid has to a protein-protein interaction. The structure is very >>complex, >> so pulling along a reaction pathway is out of the question, thus an >> alchemical path might work. >> >> I wish to integrate from state A to state B. The number of atoms in the >> wild type amino acid of state A are fewer that those in the mutant amino >> acid of state B. The example given in section 5.7.4 of the manual >> demonstrate integrating from propanol to pentane, but due to the >>GROMOS-96 >> FF each topology shares the same number of atoms. Atom PC2 and PC3 of >> state A does not require redefining in typeB chargeB and massB, they are >> transferred across as they are in both structures. How does one define a >> mixed A B topology when the number of atoms differ? I.e., if those two >> atoms in the above example were not needed in state B. >> > >You need to define transformations between dummy and real atoms. Look >into the >pmx program (this was mentioned on the list just the other day for an >identical >problem). > >-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.