[gmx-users] GMX-compatible DNA coordinates

[Tsjerk Wassenaar]

Hi Alex,

You've solved the issue of getting a DNA structure, but now you're facing a
problem of getting Gromacs to prune it. That has to do with the naming
scheme mainly. Your best bet is using sed to do name substitution. Probably
google will give some good hints about such substitutions in PDB files.

Cheers,

Tsjerk
On Apr 3, 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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