On 10/4/19 4:52 AM, Olga Press wrote:
Prof. Lemkul thank you for your response. I'm using the output file from the charmm gui site after the MD production, which contain an equilibrated DOPC bilayer with TIP3 molecules as the solvent (and I remove the ions before the solvation). I used the second option of the gmx_solvate (solvate a solute configuration) Do you suggest to remove the water molecule, than concatenate the protein coordinates with the lipids coordinates and than solvate it with water?
Yes, otherwise reposition the protein so it is further away from the membrane and does not lead to lipid deletion.
-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.
