Hallo Abhilasha Thakur, (I am not a Gromacs user, but I'll nevertheless try to answer)
You'll have to identify the Amber99 forcefield topology file, and read it to find out the naming of RNA atoms in that file. The error message asks you to change (e.g. using an editor) the atom names in your input file S_000001.pdb such that they match the atom names used in that topology file. Possibly, the atom O5P in your input file should be called O5', or that atom is missing. Hope this helps! Merry Christmas, Kay On Fri, 23 Dec 2022 15:26:15 +0530, Abhilasha Thakur <[email protected]> wrote: >Hello Everyone!! > >I am working on RNA structure simulation but I got an error on first step >to create topology file through this command "gmx pdb2gmx -f S_000001.pdb >-o S_00000_proc.gro -ignh" its showing > >*FATAL error: Fatal error:Residue 1 named A of a molecule in the input file >was mapped to an entry in the topology database, but the atom O5' used in >that entry is not found in the input file. Perhaps your atom and/or residue >naming needs to be fixed.* > >I have checked online for this error and could not find how to solve >this... Kindly suggest me what to do >*For Force field I have choose Amber99 (4th option)* > >*For water model TIP3P * > > >*PFA, the picture of error and RNA str file * >*Kindly suggest me how to solve this topology error* > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
