On 19/03/11, maria goranovic <mariagorano...@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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