On 11/29/19 3:27 AM, Mijiddorj B wrote:
Dear Justin, As you suggested, I generated the charmm36 parameter using cgenff for single unit with two capping groups. After that, I created 3 residues based on the parameter of cgenff including N-ter side, Middle, and C-ter side residues. However, the net charges of these residues are not equal to zero as -0.002, -0.004, and -0.002, respectively. 1. How can I adjust the charge of these residue?
Your model compound surely didn't have a net -0.008 charge, so make sure you're assigning charges correctly. Without seeing your actual residue definitions, there's nothing I (or anyone else) can suggest.
2. Is it possible to run simulation ignoring the grompp comments?
When grompp tells you there's a problem, don't ignore it. If you're trying to simply override these unphysical charges, your simulation will be useless because your model does not reflect reality.
-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.
