Re: [gmx-users] Dealing with residues not in the topology database

In addition to what Justin has said there are parameters for GTP to use with the amber forcefields, see: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Obviously you need to convert these from an amber format to a gromacs one. Do note that an additional atom type for the terminal anionic

Re: [gmx-users] Dealing with residues not in the topology database

Travis Craddock wrote: Hello, I am a new GROMACS user. My aim is to simulate the protein tubulin with a GTP molecule present. When attempting to create a topology file I receive a Fatal Error stating that the "Residue GTP is not found in the topology database". I understand that GTP is not

[gmx-users] Dealing with residues not in the topology database

Hello, I am a new GROMACS user. My aim is to simulate the protein tubulin with a GTP molecule present. When attempting to create a topology file I receive a Fatal Error stating that the "Residue GTP is not found in the topology database". I understand that GTP is not parameterized for the force