On 10/26/14 4:32 PM, Agnivo Gosai wrote:
Dear Users I am following the Umbrella Sampling tutorial by Dr. Lemkul and would like to have one of my doubts addressed :- After using pdb2gmx on the supplied pdb file , a topology file is obtained specifying the topology files for different protein chains in .itp format.. Inside the .itp files the inclusion of a "position restraint file" is also specified as follows :- ; Include Position restraint file #ifdef POSRES #include "posre_Protein_chain_B.itp" #endif And lastly there are .itp format position restraint files for each of the protein chains. In the tutorial it is stated that : Modify topol_Protein_chain_B.itp to include the following lines (at the end of the file): #ifdef POSRES_B #include "posre_Protein_chain_B.itp" #endif My question is :- Should I modify POSRES as POSRES_B or should I keep both portions by including the new lines at the end?
Add a new #ifdef block. You will see the convenience of restraining all protein chains or just one selectively as you do the tutorial.
-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.
