Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp
Thank you Justin! I delete the phosphate group and the problem is resolved ! Best regards Sting From: Justin Lemkul Date: 2020-04-26 00:20:44 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp> > >On 4/25/20 12:18 PM, Tingguang.S wrote: >> Dear all, >> >> >> When I generated the amber99sb force filed topology of a DNA molecule >> with gmx, a error code appeared: "Atom P in residue DA 1 was not found in >> rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P >> atoms in all the 5' nucleic acid residues in dna.rtp. >> Can some one help me with this ? > >DNA is not typically phosphorylated on its 5'-hydroxyl. Synthetic >nucleotides sometimes are, but the force field is designed for typical >biologically relevant structures. If the 5'-phosphate is relevant (which >it can be), you need to build your own .rtp entry or terminal database >entry. > >-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.
Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp
On 4/25/20 12:18 PM, Tingguang.S wrote: Dear all, When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the 5' nucleic acid residues in dna.rtp. Can some one help me with this ? DNA is not typically phosphorylated on its 5'-hydroxyl. Synthetic nucleotides sometimes are, but the force field is designed for typical biologically relevant structures. If the 5'-phosphate is relevant (which it can be), you need to build your own .rtp entry or terminal database entry. -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] Why there is no phosphorous atom in the "DA5" residue in dna.rtp
Dear all, When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the 5' nucleic acid residues in dna.rtp. Can some one help me with this ? -- 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.
