[gmx-users] help

Prajisha Sujaya prajishasujaya at gmail.com
Wed Sep 4 12:04:47 CEST 2013

 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
how to rename the atom in coordinate file

kindly give valuable suggestion how to rectify this error,

Awaiting For your reply

Thanking You

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