[gmx-users] Software for PDB input for GROMACS

[Dan Gil]

Thank you, it works great! I just had to rename the nucleic acids with the
prefix "D" (e.g. A to DA, G to DG ...).

On Fri, Nov 3, 2017 at 7:44 PM, Thomas Piggot <t.piggot at soton.ac.uk> wrote:

> The nucleic acid builder should do what you want:
>
> http://structure.usc.edu/make-na/
>
> Cheers
>
> Tom
>
>
> On 03/11/17 19:54, Dan Gil wrote:
>
>> Hi,
>>
>> I would like to use the parmbsc1 force field to simulate DNA. I installed
>> the force-field and am now actually running a simulation with a Drew
>> Dickerson Dodecamer structure I downloaded from the RCSB database.
>>
>> Now I would like to generate my own structures and simulate them. I tried
>> using Avogadro, but the software is not following the same conventions as
>> parmbsc1 and therefore failing at pdb2gmx.
>>
>> Do you have recommendations on how to generate a PDB structure for nucleic
>> acids? I suppose I could do this by hand, but I would very much like to
>> avoid this path if I can.
>>
>> Best Regards,
>>
>> Dan
>>
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
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