I would like to run molecular dynamics of a protein in which I have many calcium ions and disulfide bonds present . Now there are 2 problems:
1) Why when running GROMOS53a6 forcefield, it says "warning: all connect records are ignored" while I would like the connect records for the disulfide bonds to get included.
2) How can I fix the position of the all the calcium present in the protein so that they don't run out of the protein during simulations. Note: the calcium lacks the connect records.
All Gromacs programs ignore CONECT records and instead use the force field's definition of what should be bonded.
Distance restraints are easy to implement (see the GROMACS manual), but the biggest question you have to ask is if the force field is adequately parametrized to handle interactions with ions. Divalent metals are a problem for most additive models. I know there were recent (well, a few years ago) OPLS-AA modifications to handle carboxyl-Ca2+ interactions that highlighted common deficiencies. Evaluate available force fields carefully; I don't know how well GROMOS96 53A6 works in such cases.
Hi,
1) Have you been using the -ignh option of pdb2gmx? The use of this option does lead to the above-mentioned warning.
For retaining the disulphide bonds, you can either use the -ss option in pdb2gmx for fixing their existence or interactively do the same using the -inter option.
2) As for Calcium, it shouldn't be any problem.
I had worked on a system with Zn ion in a similar scenario and faced no problem.
Cheers
All Gromacs programs ignore CONECT records and instead use the force field's definition of what should be bonded.
Distance restraints are easy to implement (see the GROMACS manual), but the biggest question you have to ask is if the force field is adequately parametrized to handle interactions with ions. Divalent metals are a problem for most additive models. I know there were recent (well, a few years ago) OPLS-AA modifications to handle carboxyl-Ca2+ interactions that highlighted common deficiencies. Evaluate available force fields carefully; I don't know how well GROMOS96 53A6 works in such cases.
Hi,
I don't possess the details about that experiment.
Nevertheless, you can go through the following tutorials for additional help and understanding.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
All the best.
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