United-atom force fields do not consider hydrogen atoms on aliphatic (nonpolar) groups. Polar H atoms (amides, alcohols, etc) are explicitly represented to properly model hydrogen bonding.

The C-terminus is protonated however you specify; it is not true that you have to use COO- in a united-atom force field, but most biomolecular simulations are done at physiological pH so the C-terminus is in its conjugate base form. A carboxylic acid proton is by definition polar so it is not eliminated by convention.

Justin Lemkul sir please have a look at the attached figure. Simulation was carried out in 54A7.ff

Do you think using united atom ff could be the reason of this binding? I have selected GLU ASP residues in this figure.

And by COOH i was refering to side chain of ASP and GLU, not C terminal, sorry for that.

The small molecules are hydrogen-bond donors via their -OH moieties and the acidic residues are acceptors. That will be the same in any force field as Glu and Asp should always be anionic at physiological pH. Your outcome is not a unique consequence of using a united-atom force field.

Justin Lemkul

Sir,

Once bound these small molecules doesn't separate at all throughout production run. Also, Due to abundance of acidic abundance residues in my protein most of small molecules are occupying pore region, leaving me short of small molecules for further simulation analysis. This binding is also occupying pore entrance which is hindering passage of other molecules through pore. What can i do for it? should i try different pH?

I don't know what the expected physical behavior is. You need to carefully parametrize any nonstandard species and verify that its interactions with protein moieties agree with some known quantity. If you don't have that justification, you can't prove if your simulation outcomes are reasonable or not.

Justin Lemkul

sir I am interested in permebility of these small molecules across protein channel.