thanks Prof. Justin On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul <jalem...@vt.edu> wrote:
> > Please use an appropriate subject line. > > On 11/12/19 5:29 AM, shakuntala dhurua wrote: > > hello, > > Here I want to generate arg.pdb to arg.gro by using amber99sb force > field . > > for test i have used 1 residue of arginine but i got Fatal error: > > There is a dangling bond at at least one of the terminal ends and the > force > > field does not provide terminal entries or files. Fix your terminal > > residues so that they match the residue database (.rtp) entries, or > provide > > terminal database entries (.tdb). and following is the attach pdb format > > which i have used for pdb2gmx ,please suggest me to solve this problem > > AMBER does not support zwitterionic forms of single amino acids, at > least not within GROMACS. There may be a way to create such residues > from the AMBER parameter database, but you'll have to look into > published works on their force field parametrization to see if such > residue definitions exist. > > -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. > -- 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.