[gmx-users] Problems in the modelling of interaction between peptide and copper
m21.tang at qut.edu.au
Thu Apr 23 08:53:18 CEST 2015
I got a problem when modelling the interaction of a peptide and copper. I am using the force field of opls-aa. The charge of copper atoms are defined as zero and the non-bonded parameters are obtained from the CU ions, which can be found in opls-aa.
I applied smd and found that the peptide is approaching the copper surface and stopped when it is very close to the surface, due to some abnormal interaction. The whole process seems quite reasonable, however, when I rerun the simulation to obtain the interaction energy, for the vdw interaction between peptide and copper is zero, absolute zero, in the whole process.
Can anyone give me some suggestions? Is my model reasonable? I am not so confident with modelling strategy of using the LJ parameters for copper bulk material. Also the zero interaction energy is another big issue.
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