Hello Gromacs users, I want to obtain the topology file (topol.top) for this peptide Ace-Ser-Ser-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-Sep-Sep-Asp-NH2. I am using this ffG43a1p force field and this command pdb2gmx -f sereno2.pdb -o pep5-dpp-cap-linear-phospho_newbox_up_rotate.gro -ignh -ter -water spc I obtained the next error and warnings:
Identified residue ACE1 as a starting terminus. Warning: Residue SEP5 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP6 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue ASP7 in chain has different type (Protein) from starting residue ACE1 (Protein). Warning: Residue SEP8 in chain has different type (Other) from starting residue ACE1 (Protein). Warning: Residue SEP9 in chain has different type (Other) from starting residue ACE1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1021 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. According to my pdb file (www.dropbox.com/s/kihycqde78wy787/sereno2.pdb) my peptide is a continuous. I do not know how to figure out this mistake. I will appreciate if someone give me a hint. Thank you in advance, Eduardo ----- Eduardo Villarreal RamÃrez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-takes-phosphoserine-as-terminal-ends-tp5011684.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
