Dear Justin, Thank you very much your help.
Best regards, Miji > ------------------------------ > > Message: 2 > Date: Tue, 23 Jan 2018 06:44:59 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Atom OT1 in the residue > Message-ID: <82fdffdd-85b4-56ab-8445-27f6ca0aa...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 1/23/18 1:59 AM, ????? ????????? wrote: > > Dear gmx user, > > > > I am using gromacs 5.1 with charmm36-march2017 force field. I have an > error > > as following: > > > > "Atom OT1 in residue DTRP 4 was not found in rtp entry DTRP with 24 atoms > > while sorting atoms." > > > > How can I fix this error? > > > > Additionally, I modified the structure of last DTRP residue from the TRP > > residue. I guess that there is no structural problem. > > > > The D-amino acids are not in residuetypes.dat, so you probably have a > false chain termination and the patching gets screwed up. See step 5 in > http://www.gromacs.org/Documentation/How-tos/Adding_ > a_Residue_to_a_Force_Field > > This holds true for anything non-standard. We've made the error message > clearer in the latest release. > > -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.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.
