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

[maria goranovic]

is this a bug of some kind then? someone ? anyone?

just bumping,

maria

On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic
<mariagoranovic at gmail.com>wrote:

> 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
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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