[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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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