Thank you so much for the guide Justin! The path looks clearer to me now :) Ming
On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/15/18 2:56 PM, MD wrote: > >> updated, I figured it is because my N and CA have different type names >> than >> charmm, which is weird cause I used CHARMM GUI to get the itp files for >> the >> modified amino acid. Would it be an easy fix if I manually change those >> two >> atom names or I should go a different route for the cmap problem? >> > > CHARMM-GUI can only parametrize a species via the interface to CGenFF. > This is not appropriate for integral residues in a polypeptide chain. The > backbone of each amino acid is the same; yours has different atom types > (presumably from CGenFF) that are not the same as the normal types. This > makes the application of CMAP parameters impossible. > > You should separately parametrize your side chain using CHARMM atom types; > the initial charges provided by CGenFF can be used as a first guess but > should be subject to refinement as needed. A proper parametrization > protocol will involve vibrational analysis, dipole moment analysis, water > interactions, and conformational energy scans. It is laborious but if you > want a custom residue to be consistent with the highly optimized protein > force field, you have to do the work. > > -Justin > > Thanks, >> >> Ming >> >> On Mon, Jan 15, 2018 at 1:34 PM, MD <refm...@gmail.com> wrote: >> >> Hi Gromacs folks, >>> >>> I have a modified amino acid which has all the parameters set. However, >>> the last error is the "cmap torsion between atoms xxxxxxx" and it would't >>> go away. Basically the cmap contains atoms of C-N-CA-C-N from three >>> residues, where the CA is my newly modified residue. THe only thing I >>> could >>> think of is the newly modified residue was not recognized by gromacs, >>> but I >>> have checked the residue.dat, the log from pdb2gmx and it looks like this >>> residue was not considered "alien". Got stuck here any help will be >>> appreciated! >>> >>> Best, >>> >>> Ming >>> >>> > -- > ================================================== > > 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.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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. > -- 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.