[gmx-users] *.ITP file

[Justin A. Lemkul]

On 5/13/12 5:54 AM, Kowsar Bagherzadeh wrote:
> Dear Users,
> I am trying to generate an *.ITP file for a ligand I am studying using Prodrg
> server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar
> hydrogens) while the *.ITP file dispays 37 atoms and it does not display the
> double bond in the structure, which results in an error in simulation. Other
> files that Prodrg gives like DRGAPH.PDB display 37 atoms same as the *.ITP file
> and they also do not display the double bond in the structure ! only the
> DRGFIN.PDB with 41 atoms ( all hydrogens) displays the double bond. I have used
> Prodrg several times before and this is the first time it happens. are there any
> other online services or any software for the purpose? Thank you
>

Whether or not any file "displays" a double bond is irrelevant.  There will not 
be duplicate bonds in the .itp file, nor will a double bond necessarily appear 
in visualization software, though some programs may try to guess.

The most important things to do are obtain the coordinate file that matches the 
topology (e.g., the one that does not have nonpolar hydrogens, per Gromos 
convention) and realize that you will need to do a fair bit of work to improve 
the PRODRG topology: http://pubs.acs.org/doi/abs/10.1021/ci100335w

ATB is another option.  It is newer and performs better.

http://compbio.biosci.uq.edu.au/atb/

-Justin

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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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