I need to run a molecular dynamics simulation in gromacs with a peptide that has an acetylate Lys residue. This residue is not in topology database (GROMOS96 43a1 force field). How can I generate the topology file?
Adding new residue to the topology database requires the following steps:
1. go to the gromacs database directory cd /usr/share/gromacs/top/gromos43a1.ff/
2. amino acid topology is highlighted in aminoacids.rtp file (open and see how topology is presented)
3. then prepare your topology for modified amino acid and insert just like that format. be careful because format plays critical role.
4. hydrogen bonds also has to be inserted to the aminoacids.hdb file.
5. if you introduce new atom type is should be also indicated in ffnonbonded.itp and ffbonded.itp file.
6. go to the directory cd /usr/share/gromacs/top and modify residuetypes.dat and phbres.dat file as well.
in the final step you can generate your topology for the peptide using standard gromacs command pdb2gmx -f input.gro (or input.pdb)
If you have further question just let me know.
Adding new residue to the topology database requires the following steps:
1. go to the gromacs database directory cd /usr/share/gromacs/top/gromos43a1.ff/
2. amino acid topology is highlighted in aminoacids.rtp file (open and see how topology is presented)
3. then prepare your topology for modified amino acid and insert just like that format. be careful because format plays critical role.
4. hydrogen bonds also has to be inserted to the aminoacids.hdb file.
5. if you introduce new atom type is should be also indicated in ffnonbonded.itp and ffbonded.itp file.
6. go to the directory cd /usr/share/gromacs/top and modify residuetypes.dat and phbres.dat file as well.
in the final step you can generate your topology for the peptide using standard gromacs command pdb2gmx -f input.gro (or input.pdb)
If you have further question just let me know.
Thanks for the advice. Nevertheless, I found force field for amino acids with post-translational modifications, which make easier the task.
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003154
Files are available at http://vienna-ptm.univie.ac.at/
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