[gmx-users] no inter-residue bonds for nucleotides defined in ffG43a1 ?

Michael Brunsteiner mbx0009 at yahoo.com
Sat Nov 6 18:25:03 CET 2004

Dear all,

ffG43a1 seems to include topologies for various nucleotides.
After reordering the atoms in the pdb file (or alternatively
the rtp-entry) and renaming the residue names accordingly
pdb2gmx seemd to work and gives me a topology file. 
Problem is: it does not find the covalent bonds between two 
nucleotides. looking at the rtp file i find that, e.g., for 
DGUA there is a bond "O3*    +N" defined, but no "O3*    +P". 
If I add the bond to the rtp file, pdb2gmx finds it but will not 
find parameters for most of the angles and dihedrals resulting 
from this bond.
Does that mean that the implementation of necleotides in
ffG43a1 can only be used for nucleotides that are bonded to
peptides (as opposed to each other) ? 
Or did I overlook something here ?

another question: in a previous mail in this newsgroup I read
that the developers plan to add support for nucleotides in oplsaa
is this project anywhere near completion ?


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