[gmx-users] importing RNA

Ken Rotondi ksr at chemistry.umass.edu
Fri Jan 7 16:46:40 CET 2005


I changed 49 to 53 at the beginning of aminoacids.dat. No change in 
behavior. I was written off list and told that the only work around is 
re-naming the bases in the .pdb file. Was also told to pursue using 
OPLS, as this is a better ffield for nucleic acids. So in the second 
vein, does anyone have experience, advice for using OPLS with nucleic 



On Jan 7, 2005, at 9:44 AM, Berk Hess wrote:
>> Okay,
>> 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.
> Berk.

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