On 2/18/19 11:39 AM, Shweta Kumari wrote:
Dear gromacs users, I have protein-membrane (POPC only) system. I want to replace the cholesterol molecules with POPC but outside a 2.5nm cutoff distance of protein surface. I am using this command : gmx insert-molecules -f system.gro -ci cholesterol.pdb -nmol 10 -try 10 -replace POPC -o output.pdb But this command randomly select the POPC molecules and replace it with cholesterol. In this way few cholesterol molecules are coming near the protein (within 2nm). Thanks in advance!
Use gmx select to create an index group of POPC molecules that satisfy the geometric criterion, and use that as your replacement group.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
