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

[Mark Abraham]

On 22/03/2011 8:15 PM, maria goranovic wrote:
> is this a bug of some kind then? someone ? anyone?

It's still hard to say. I asked you for your GROMACS version and input 
coordinate file, and you didn't give us either (in full). While you're 
there, what pdb2gmx command did you use?

Mark

> just bumping,
>
> maria
>
> On Mon, Mar 21, 2011 at 10:17 AM, maria goranovic 
> <mariagoranovic at gmail.com <mailto: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 <mailto:mark.abraham at anu.edu.au>> wrote:
>
>
>
>         On 19/03/11, *maria goranovic * <mariagoranovic at gmail.com
>         <mailto: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.
>
>
>>
>
>         Mark
>         --
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>
>
>
>     -- 
>     Maria G.
>     Technical University of Denmark
>     Copenhagen
>
>
>
>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen

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