Consistent H-bonding, but not in Decomp Analysis
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Uddipta Ghosh Dastidar
Apr 15, 2025, 4:35:20 AMApr 15
to gmx_MMPBSA
I have run an MD Simulation of 200ns, and residue Asp555 (chain A) consistently showing H-bonding in all frames.
However, in the Decomposition Analysis, in gmx_MMPBSA, that residue Asp555 (ChainA) showing very less contribution.
However, in the Decomposition Analysis, in gmx_MMPBSA, that residue Asp555 (ChainA) showing very less contribution.
What can be the possible reason and explanation?
mariosergi...@gmail.com
Apr 15, 2025, 11:49:52 AMApr 15
to gmx_MMPBSA
It may seem a bit counterintuitive, but it can make sense. I'll try to explain my point of view with the context I have (it doesn't necessarily have to be an absolute truth).
Reviewing the structure, I notice that A:APS:555 does indeed have what appears to be a hydrogen bond. I'm not sure if the angle could be affected by the mobility of the acceptor and donor groups, which could affect the energy (which seems to happen given that the SD is the highest of all the residues computed).
Structurally, there is a hydrogen bond; however, there are other important considerations. First, the hydrogen bond present is one of the weakest (https://www.pharmacy180.com/article/classification-of-hydrogen-bonding-2067/).
Second, the residue is in a fairly favorable context when not interacting with the ligand. In that case, the residue A:ASP:555 can interact by hydrogen bond with A:LYS:432 or with the bb of others, such as A:LUE:557, in both cases with similar types of interactions, and therefore similar energy values. From an energetic point of view, if the residue is sufficiently stable in the receptor, it does not necessarily have to contribute greatly to the complex. According to the energy file in both the complex and the receptor, the residue has similar interaction energies, so the delta is small.
It is difficult to explain with such little information, but I hope it helps you understand the numbers you get. If you do not feel this is correct, it is advisable to use other methods for calculating and clarifying your doubts.
Reviewing the structure, I notice that A:APS:555 does indeed have what appears to be a hydrogen bond. I'm not sure if the angle could be affected by the mobility of the acceptor and donor groups, which could affect the energy (which seems to happen given that the SD is the highest of all the residues computed).
Structurally, there is a hydrogen bond; however, there are other important considerations. First, the hydrogen bond present is one of the weakest (https://www.pharmacy180.com/article/classification-of-hydrogen-bonding-2067/).
Second, the residue is in a fairly favorable context when not interacting with the ligand. In that case, the residue A:ASP:555 can interact by hydrogen bond with A:LYS:432 or with the bb of others, such as A:LUE:557, in both cases with similar types of interactions, and therefore similar energy values. From an energetic point of view, if the residue is sufficiently stable in the receptor, it does not necessarily have to contribute greatly to the complex. According to the energy file in both the complex and the receptor, the residue has similar interaction energies, so the delta is small.
It is difficult to explain with such little information, but I hope it helps you understand the numbers you get. If you do not feel this is correct, it is advisable to use other methods for calculating and clarifying your doubts.
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