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

[Domenico Schitti]

Hi Tsjerk, 
thank's for you help! 
I followed your instructions (really helpful), then I performed a solvation. When I tried to use "grompp" I got this error:

"number of coordinates in coordinate file (speptideh.gro, 32884)
does not match topology (speptide.top, 2602)"

I tried to change the x number in the .top file, under [molecules], just at the end of it:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
DHT                        x

..But cant fix it.

Thank you again!
Best regards,
Domenico.

> Date: Sat, 16 Jan 2016 11:30:50 +0100
> From: tsjerkw at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem with DHT residue not found.
> 
> 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.
> -- 
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