[gmx-users] Loss of GTP in topology file.

[Daniel Adriano Silva M]

> Hi,
> I have added missing atoms to my pdb file through servers of WHATIF,when I
> use the force field option then the following output comes in shell console:
> Fatal error:
> Residue 'GTP' not found in residue topology database
> and the following files are created:
>  2a5f.top  2a5f_A.itp  2a5f_B.itp  posre_A.itp  posre_B.itp
> Please guide me so that GTP is added to PDB.Further which force field and
> box will be better for my simulation of enzyme-Protein GTP complex?
> regards,

I guess you are missing that GTP could be considered as an additional
compound (if you are simulating proteins), and as long as you can see
it is not included on Gromacs Building Blocks
(http://www.gromacs.org/index.php?option=com_content&task=view&id=78&Itemid=97)

then Gromacs cannot create automatically the topology for this
compound, instead you need to create the topology (or search for a
previously created one), I thin you can use the PRODRG server to
accomplish this task. Take a look in the manual about how to use your
own topologies, also you can take a look here:

http://wiki.gromacs.org/index.php/Errors

> Please guide me so that GTP is added to PDB.Further which force field
> and box will be better for my simulation of enzyme-Protein GTP complex?

I agree with Mark, "this is not a simple question, and you need to
search the literature thoroughly to see what other people have done
for systems similar to yours and consider their reasons", then I
recommend you to follow Mark's advice.


2008/2/18, Mark Abraham <Mark.Abraham at anu.edu.au>:
> s lal badshah wrote:
> > Hi,
> > I have added missing atoms to my pdb file through servers of WHATIF,when
> > I use the force field option then the following output comes in shell
> > console:
> > Fatal error:
> > Residue 'GTP' not found in residue topology database
> > and the following files are created:
> >  2a5f.top  2a5f_A.itp  2a5f_B.itp  posre_A.itp  posre_B.itp
>
> Please describe what you're doing here, with actual console input. If
> you were using pdb2gmx and got this fatal error, then there these .top
> and .itp files will not have been created by pdb2gmx.
>
> See
> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
> for discussion of this pdb2gmx error message.
>
> > Please guide me so that GTP is added to PDB.Further which force field
> > and box will be better for my simulation of enzyme-Protein GTP complex?
>
> This is not a simple question, and you need to search the literature
> thoroughly to see what other people have done for systems similar to
> yours and consider their reasons.
>
> Mark
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