On 9/5/18 9:25 AM, milad bagheri wrote:
I'm going to examine the interaction between the two proteins using molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 from the rcsb , which has two protein(Complex). I want to create a gap between two protein, and then with the same coordinate Put these two proteins in a box and run MD 100 nanoseconds, for validation this trick compare rmsd x-ray pose and Md pose. please help me ...
Separate the coordinates of the two proteins, translate one of them with editconf, and concatenate the new coordinates back together.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.