Re: [gmx-users] Atom OT1 in the residue
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 > 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.
Re: [gmx-users] Atom OT1 in the residue
On 1/23/18 1:59 AM, Мижээ Батсайхан 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.
Re: [gmx-users] Atom OT1 in the residue
On Tue, 23 Jan 2018 at 3:59 PM, Мижээ Батсайхан wrote: > Thank you for your answer. I modified the L-TRP structure to D-TRP > structure, and the last version of charmm36 contains a topology of D-TRP. I > used that one. Check for the naming of OT1 in the residue topology database of Dtrp > > Thanks. > > > > > > 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. > > > > > > > Hi > > > > If you have modified the structure, then definitely you need to generate > a > > topology file for that molecule. > > Thank you > > > > > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Atom OT1 in the residue
Thank you for your answer. I modified the L-TRP structure to D-TRP structure, and the last version of charmm36 contains a topology of D-TRP. I used that one. Thanks. > > 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. > > > > Hi > > If you have modified the structure, then definitely you need to generate a > topology file for that molecule. > Thank you > > -- 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] Atom OT1 in the residue
On Tue, Jan 23, 2018 at 12:29 PM, Мижээ Батсайхан 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. > Hi If you have modified the structure, then definitely you need to generate a topology file for that molecule. Thank you > > > Best regards, > > Miji > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Atom OT1 in the residue
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. Best regards, Miji -- 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.
