[gmx-users] Problem with DHT residue not found.

[Tsjerk Wassenaar]

Hi Domenico,

- Extract the DHT residue(s) from the PDB file and save it to a separate
file (DHT.pdb).
- Convert DHT.pdb to DHT.gro
- Run pdb2gmx on the protein PDB file; you'll get the GRO and TOP file
- Add the coordinates from DHT.gro to the protein GRO file and update the
number on the second line of the GRO file (adding the number of atoms from
DHT.gro)
- Add a line #include "DHT.itp" before the [ system ] directive in the TOP
file
- Under the [ system ] directive, add DHT with the number of them you have
in the GRO file now. Just note that the order of molecules here needs to be
the same as the order of molecules in the GRO file.

If you need to do this more, I might have an automated workflow taking care
of these things...

Cheers,

Tsjerk


On Sat, Jan 16, 2016 at 9:11 AM, Domenico Schitti <dom.90 at hotmail.it> wrote:

> Dear Gromacs Users,
>
> I have to run an md simulation for the 1I37.pdb file, but when I try to
> get a topology gromacs give me that error:
>
> Fatal error:
> Residue 'DHT' not found in residue topology database
>
> So I downloaded a DHT.itp from ATB online but I dont understand how to
> properly use it for solve my problem in the fastest way possible.
>
> I tried to delete all DHT entries from the .pdb file, generating a
> topology file.
> Then I write #include "dht.itp directory" on the topology made from that
> modified pdb file.. But I think thats wrong.
>
> I read the manual but cant understand well what to do.
> Can you please give some suggestions?
>
> Thank you.
>
>
> Best regards,
> Domenico Schitti,
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-- 
Tsjerk A. Wassenaar, Ph.D.