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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