Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Hi, If you are using any of the united atom GROMOS96 forcefields then there is already an rtp entry for ATP. Check out the .rtp files in the top folder. All you need to do is to have the ATP atoms in the pdb file the same as the atom names in the .rtp file for pdb2gmx to do all the work for yo

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Be aware, that you can't use the ouput with every forcefield... Attaching the gro-file to your protein gro at the proper position (right after the protein) and building the correct topology should do the job. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical &

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Yes, I found a server (ProDrg) can get the .gro and .top files of ATP molecule. --- Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Ins

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

As Mark suggested. If you have the parameters for your ATP, build an RTP-entry and afterwards, give the protein together with ATP into pdb2gmx... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettinge

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Thank u very much for your suggestion, and now I had get the .gro file and .top file of ATP molecule, but how to I add the ATP molecule into the .gro and .top files of the protein? (If I paste the ATP's datas to the end of protein's file directly, and do genbox, then the result (.gro /.top file) on

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goetti

Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[EMAIL PROTECTED] wrote: > Dear GROMACS users: > I want to simulate a complex composed by a protein and an ATP molecule, > and when I use the pdb2gmx to build the topology file and transfer > the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue > ATP 1 not found in rtp entry wi

[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Dear GROMACS users:I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer thepdb file to gro file, it said "Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms", So how can