[gmx-users] help

Justin Lemkul jalemkul at vt.edu
Wed Sep 4 12:30:50 CEST 2013

On 9/4/13 6:04 AM, Prajisha Sujaya wrote:
>   I am facing a problem while simulating the tRNA molecule
> while converting pdb to gro,
> Fatal error:
> Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
> while sorting atoms.
> force field used  3 (AMBER96 protein, nucleic AMBER94), water model TIP3P.
> i checked in gromacs error list, in that they mentioned simply re-name the
> atoms in your coordinate
> file<http://www.gromacs.org/Documentation/File_Formats/Coordinate_File>
> ,
> how to rename the atom in coordinate file

Use a text editor.



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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