[gmx-users] importing RNA

Berk Hess gmx3 at hotmail.com
Fri Jan 7 15:44:38 CET 2005

>From: Ken Rotondi <ksr at chemistry.umass.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] importing RNA
>Date: Fri, 07 Jan 2005 09:34:51 -0500
>I looked in the aminoacids.dat file and found none of the nucleotides 
>listed, just, as the name would imply, aminoacids. None-the-less, I added 
>A, U, G, and C at the end of the file.
>pdb2gmx behavior is unchanged: the .pdb is read, the xlateat.dat is 
>converted successfully, the chains and lengths are correctly listed, all 
>occupancies one, it begins processing chain 1, converts specbond.dat 
>successfully, then...
>Fatal error: Residue 'U' not found in residue topology database

Note that you also need to add 4 to the number on the first line.


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