[gmx-users] GMX-compatible DNA coordinates

[Mark Abraham]

Hi,

I tried that search myself and found some things that looked potentially
useful to you, so I suggested that search. Either you might find something
useful there, or the dialogue could progress about what you need. Requiring
perfect input for pdb2gmx is a fairly stringent expectation.

Mark
On 03/04/2015 3:40 pm, "Alex" <nedomacho at gmail.com> wrote:

>  Mark,
>
>
> Not to troll, but why did you assume that I didn't do my due diligence
> before posting here?
>
> Because, you see, you could have left that second part of your reply
> (which only confirms the legitimacy of my initial question), and it would
> make it less insulting.
>
>
> Alex
>
>
>
>   >
>
> Hi,
>
> Googling things like "gromacs DNA structure" is a good bet. There are no
> fully standardised naming schemes or workflows, so you will likely not have
> something do everything for you.
>
> Mark
>
> On 03/04/2015 7:03 am, "Alex" <nedomacho at gmail.com> wrote:
>
>
> I'm fully aware that this is a forum for discussing Gromacs, but there's a
> bit of a frustrating situation that involves using it.
>
> I need a linear ssDNA chain, sequence of my choosing, anything that will
> work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
> for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>
>
> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
>
> I will really appreciate any suggestions.
>
>
> Thank you,
>
>
> Alex
>
>
>
>
> --
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> Best regards,
>
>  Alex                            mailto:nedomacho at gmail.com
> <nedomacho at gmail.com>
>
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