Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error
On 10/3/19 8:57 PM, Mijiddorj B wrote: 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? Yes. -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.
Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error
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 > 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.
Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error
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.
[gmx-users] Adding a new residue and Duplicate atom index () in angles error
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? Best regards -- 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.
