[gmx-users] single RNA nucleotide in CHARMM with phosphate problem with pdb2gmx

[maria goranovic]

Dear All

I am trying to generate a topology for guanosine monophosphate: i.e. an RNA
base with a phosphate at the 5' Carbon. I tried to read in a pdb file
containing all atoms, and used pdb2gmx with CHARMM. However, the output
coordinate file has no phosphate group on it. Why does the phosphate
disappear, and why does pdb2gmx not even give me a warning?

Assuming that a molecule like GMP does not have a topology, I am guessing I
might have to make a new residue within CHARMM. that should not be too much
work because there is no new angle/dihedral/bond/atom type to be be added.
Can someone please help me with a simple workflow so I do not miss something
important?

Of course it would be best if pdb2gmx worked as it is if I just have a
single nucleotide, and not a chain?

-Maria

-- 
Maria G.
Technical University of Denmark
Copenhagen
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