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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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