Hi, to get things straight did you use pdb2gmx or just editconf? Where does the error occur?
My personal choice is Maestro which is free for academic use. The resulting pdbs' have no problem with Gromacs. If you want to make minor changes, for example change LIG to DRG (assuming DRG is mentioned in the ff) then yes you can use a text editor. ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of FL S <frank.leonard.schm...@gmail.com> Sent: Wednesday, March 8, 2017 11:01:13 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Get a correct .pdb for a synthetic peptide Hello, I want to run a gromacs MD for a small synthesized peptide. All used amino acids are known for and defined in gromacs, as are the termini. Consequently it would be ideal to use pdb2gmx to create the*.gro, *.top and *.itp, but I have troubles creating a syntactically correct *.pdb input file. I created *.pdb (or *.mol2) files using standard chemistry software such as Chem3D and Avogadro, and also tried VMD and PRODMG, but never get a *.pdb file readable by gromacs. Using editconf leads to a fatal error as all atoms are assigned to residue DRG which is not defined. Using swissparam for gives the same problem, just that now it is LIG, not DRG. (and I ideally want to work with OPLS, not CHARMM). The only option I see is to use an editor to manually change the atom numbering and to group the atoms into amino acids, but this seems very tedious. What is the usual “pipeline” you are using in order to create your own molecular structure and import them into gromacs? Is there a tutorial? I am working with gromacs 5.1.4 in a linux environment and am able to do simulations using *.pdb input files downloaded from rcsb.org. Thanks in advance -- 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.