[gmx-users] importing RNA

Ken Rotondi ksr at chemistry.umass.edu
Fri Jan 7 15:34:51 CET 2005


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

My problem persists.


On Jan 7, 2005, at 7:00 AM, Alessandra Villa wrote:

> Hi Ken,
>> I have a problem running pdb2gmx on a .pdb file that contains both RNA
>> and protein. The command returned the following error, "Residue 'U' 
>> not
>> found in residue topology database". I opened the ffG43a2.rtp file and
>> the ribonucleotides were named ADE, GUA, CYT and URA, while they were
>> named as A, G, C, and U in the .pdb file. I edited the .rtp file,
>> changing the ribonucleotide names to those in the .pdb file. Rerunning
>> pdb2gmx resulted in the same error.
> This is good, now try to add also the name of the  A, G, C, and U in 
> the aminoacids.dat
> Regards
> Alessandra

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