Dear Justin, Thank you very much for your prompt response. Do you mean that I made a mistake when I define the bonds in .rtp file?
Best regards, Mijiddorj > ------------------------------ > > Message: 6 > Date: Thu, 3 Oct 2019 15:47:13 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Adding a new residue and Duplicate atom index > () in angles error > Message-ID: <42335958-7fdd-1862-22a9-9b590d1ce...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 10/3/19 11:56 AM, Mijiddorj B wrote: > > Dear GMX experts, > > > > I am trying to prepare CHARMM36 parameter for non-standard amino acid > using > > some instructions such as > > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > and > > the user manual. > > > > After I modified merged.rtp, merged.hdb, and residuetype.data files, > > gmxpdb2gmx successfully created > > gro, topol, and posre files. > > > > However, gmx grompp could not generate the tpr file because of several - > > maxwarn. > > > > The warmings commented as"duplicate atom index (34) in angles" and > > "duplicate atom index (34) in dihedrals". > > > > I think this kind error is related to the topology file especially I need > > to change ffbonded.itp of charmm36. However, I have no idea how to change > > this file. Could you explain to me how to fix this problem? > > You have the same atom used twice in angle and dihedral interactions. > This suggests an error in your .rtp entry, probably a typo, in which the > same atom appears twice in angle and dihedral definitions. > > -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. > > End of gromacs.org_gmx-users Digest, Vol 186, Issue 5 > ***************************************************** > -- 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.