I mean it is disconnected after energy minimization, i found out the CO is not connecting with the NH from the +1 amino acid. The structure was intact before the simulation.
Ming On Mon, Jan 15, 2018 at 6:23 PM, MD <refm...@gmail.com> wrote: > Hi another quick question, what do you think could be the problem if the > modified amino acid is not connecting to the +1 amino acid? the [cmap ] in > merged.rtp already has the [ cmap ] -C N CA C +N > > 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.