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

[Mark Abraham]

On 19/03/11, maria goranovic  <mariagoranovic at gmail.com> wrote:
> 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? 
> 
> 

That does sound suspicious, but it's hard to say what went wrong. What GROMACS version was it, and what were the contents of your input coordinate file?


> 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? 
> 
> 

The procedure is outlined here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field Your case should be a reasonably straightforward exercise in assigning sensible atom types from the pre-existing options.


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

I'm not sure what you are asking here.

Mark
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