I want to perform MD simulation on a protein that contains water molecules in PDB what forcefield parameters (topology/ parameter ) files should one use ?
The same water model that you will use for filling the box later during the preparatory phase should be used with the crystal water molecules.
Ayaz Anwar thank you for your response. I have used the charm 36 protein topology file and the TIP3p water model but when I try to simulate the system I get an error regarding parameters for HT
what program you are using to run the simulation?
why do you want to keep crystal water molecules? These are often irrelevant to keep if they are not critical for your analysis.
HT of what? can you share the full error message?
Ayaz Anwar I am using NAMD. I just want to see whether these crystal water molecules affect protein simulation, so I am not removing them.
UNABLE TO FIND ANGLE PARAMETERS FOR CT1 C HT (ATOMS 1972 1985 1987)
this is the error
1972 and 1985 atoms are the last residues of protein and 1987 is the water molecule
Still, your goal is vague to me, as the water model will treat both types of water with the same parameters.
I never used NAMD, so I can not comment in detail.
The angle parameters of CT1 and C should be provided by the force field you are using. IF the NAMD is unable to find it, you should check the FF files for the naming convention (maybe you need to mention that this is the terminal residue).
Regarding HT, did you add hydrogens to your crystal water? If yes, then check the naming convention of how the water model (you are using) names H-atoms in the water molecule. If not, then what HT refers to; hydrogen or oxygen (I am guessing, it should be Hydrogen), I don't have any more ideas left to share.
Good luck
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