[gmx-users] Error using pdb2gmx tool

Justin Lemkul jalemkul at vt.edu
Thu Aug 21 13:22:01 CEST 2014

On 8/21/14, 5:24 AM, ankit agrawal wrote:
> hi,
> I was simulating A cadherin molecule (PDB ID: 4APX). I removed all the
> water molecule from molecule then ran the following command.
> pdb2gmx -f 4APX.pdb -water tip3p
> then I chose force field : CHARMM27 (with CMAP) after that it should create
> 3 types of files  (.gro, .itp, .top) but it is not generating the .gro file
> and showing an error.
> "Fatal error: Residue 'CA' not found in residue topology database".

Calcium ions are called "CAL" in CHARMM.  Rename the residue(s) in the .pdb file.



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