[gmx-users] Protein-ligand error pdb2gmx

Justin Lemkul jalemkul at vt.edu
Fri Nov 6 18:00:03 CET 2015

On 11/6/15 11:45 AM, Poncho Arvayo Zatarain wrote:
> Hello: I made the Apoferritin-T4 Lysozyme tutorial of Justin, then i change the ligand and simulated Apoferritin with an anaesthesic (halothane) and everything is fine. I tried to run a third simulation using halothane as ligand and DPPC instead of Apoferritin. I have a folder of gromos53a6.ff with all the parameters of this forcefield. But when i try to run pdb2gmx, the following error appears: Fatal error: "Residue DPP not found in residue topology database". The only different thing i did was aggregate the gromos53a6.ff folder and change Apoferritin for DPPC (i obtained DPPC.pdb and dppc.itp structure from P. Tieleman webpage). How can i solve this error? 		 	   		

Start by Googling and surely you will find 

Stock 53A6 is probably not the best choice for simulating membranes.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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