[gmx-users] help

[Prajisha Sujaya]

 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

kindly give valuable suggestion how to rectify this error,


Awaiting For your reply

Thanking You