[gmx-users] pdb2gmx takes phosphoserine as terminal ends

[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 -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 Ramírez   
Postdoctoral Research Fellow
Mineralized Tissue Laboratory,
Hospital for Special Surgery.                            


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