[gmx-users] Atom was not found

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 16:32:01 CEST 2014

On 6/18/14, 9:21 AM, h.alizadeh at znu.ac.ir wrote:
> Dear Users,
> I want to simulate a protein by GROMACS.
> When I use pdb2gmx command, topology and other files are produced from my
> pdb file.
> But when I define a box for my protein by editconf before pdb2gmx, I face
> with this fatal error:
> "Atom OXT in residue VAL 226 was not found in rtp entry VAL with 8 atoms
> while sorting atoms"
> of course as I said, without defining a box, pdb2gmx is ok!!

Defining the box alone should have no effect on what the atoms are, unless 
something has been renamed by changing formats or something.  Do a diff on the 
files before and after editconf, but there is no real reason why anything should 
have been changed, or any real reason to manipulate the box before pdb2gmx.



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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