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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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