[gmx-users] pdb2gmx takes phosphoserine as terminal ends

2013-10-07 Thread Villarealed
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

Re: [gmx-users] pdb2gmx takes phosphoserine as terminal ends

2013-10-07 Thread Justin Lemkul
On 10/7/13 4:40 PM, Villarealed wrote: 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