Thank you, Justin！
You mean that I should use the following command: "gmx pdb2gmx -f formic-acid.pdb -ter "？ I had used the flag -ter, but the program did not prompt interactive selection. Best regards Sting From: Justin Lemkul <jalem...@vt.edu> Date: 2019-03-28 21:16:22 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to create top of small molecules with pdb2gmx> > >On 3/28/19 9:15 AM, Tingguang.S wrote: >> Dear all, >> >> >> I am trying to create the topology of a system with 100 formic acid >> molecules in the box. Charmm36 force filed was used, and I noticed that the >> corresponding entry for formic acid in this force filed was residue FORH. >> When I typed the command line: gmx pdb2gmx -f formic-acid.pdb, the error >> code is: "Atom HN in residue FORH 1 was not found in rtp entry FORH with 5 >> atoms". It seems that pdb2gmx automatically added the N terminus. How can I >> avoid this auto addition of the terminus. If pdb2gmx can not be used to >> generate a small molecule top file, then how can I make use of the >> parameters which had been defined in the existed force filed files (In this >> case, the residue FORH). >> > >Interactively select terminal patching and choose "None" > >-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.
