Protein+ATP+Mg complex Amber forcefield

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No

Hello everyone,

I have been doing simulations of a protein using AMBER99sb-ILDN using Gromacs. Now, I am planning to initiate simulations of a protein-ATP/ADP complex. While searching for ATP parameters I found a few papers which employed AMBER99sb*ILDN-parmbsc0-χOL3 + AMBER99ATP/ADP force fields for protein+ATP complexes.

In Gromacs user contributions section I could find ff99sb-star-ildn.tgz and amber99sb_parmbsc0.ff.tgz. So does this mean I will have to stitch the two forcefield together for missing atoms and bonded and non bonded interactions to get AMBER99sb*ILDN-parmbsc0-χOL3 force-filed. I guess I can get the AMBER99ATP/ADP part by getting ATP/ADP prep and frcmod from amber.manchester.ac.uk and then conversion as discussed in a recent post Amber prep & frcmod files to gromacs.

thanks for your time and attention.

regards,
satti

2

Hello,

To answer my own question. After running diffs ad going through itp files, I have come to conclusion that adding few dihedrals (based on Proteins 78, 1950 (2010)) from ff99sb-star-ildn.tgz to amber99sb_parmbsc0.ff.tgz would eventually be the forcefield referred to as AMBER99sb*ILDN-parmbsc0-χOL3 in literature.

Any comments are welcome.

regards,
satti

3

Hello Satti,
I am also doing MD simulations of a protein. But I am new in this field. So I don’t know how to create a force field for Mg. My system has protein+cofactor+Mg. please suggest to me how it will work or send your Mg prepi and frcmod file.