[gmx-users] pdb2gmx takes phosphoserine as terminal ends

[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 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.

You skipped step 5 in 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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