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

[Mark Abraham]

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