[gmx-users] importing RNA
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'
>> 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
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