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

[maria goranovic]

Here are the contents of my input coordinate file.

CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
ATOM      1  P   G   A   4       5.488  -0.842   0.708  1.00  0.00
P
ATOM      2  OP1 G   A   4       6.418   0.258   1.047  1.00  0.00
O
ATOM      3  OP2 G   A   4       5.367  -1.998   1.624  1.00  0.00
O
ATOM      4  O5' G   A   4       4.010  -0.213   0.513  1.00  0.00
O
ATOM      5  C5' G   A   4       3.816   1.098   0.014  1.00  0.00
C
ATOM      6  C4' G   A   4       2.324   1.432  -0.121  1.00  0.00
C
ATOM      7  O4' G   A   4       1.623   0.448  -0.862  1.00  0.00
O
ATOM      8  C3' G   A   4       1.584   1.482   1.211  1.00  0.00
C
....
ATOM     33  H21 G   A   4      -5.974   0.099  -0.815  1.00  0.00
H
ATOM     34  H22 G   A   4      -4.841   1.428  -0.876  1.00  0.00
H


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


Here, I am wondering if the above problem is occurring because pdb2gmx is
not being able to deal with an isolated nucleotide (while it might be able
to deal with an polymer)

Maria


On Sat, Mar 19, 2011 at 5:44 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> 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_FieldYour case should be a reasonably straightforward exercise in assigning
> sensible atom types from the pre-existing options.
>
>
>
>
> Mark
> --
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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