[gmx-users] Prot_prep_problem

Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output

Re: [gmx-users] Prot_prep_problem

HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand too. However if you want to be sticked with gromos ff I do as follow: 1. prepare my system with -ignh option in pdb2gmx 2. run the simulation 3. use protonate over the pdb and the final

Re: [gmx-users] Prot_prep_problem

I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really. Regards andrea andrea spitaleri wrote: HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and

Re: [gmx-users] Prot_prep_problem

pkmukher wrote: Hello group users, I am trying to prepare a protein using the pdb2gmx module of gromacs.I have stripped the hydrogens using a different program and using a pdb file as the input.I am getting the following error message. Please help me with your suggestions on this. Thank you