[gmx-users] importing RNA

[Alessandra Villa]

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