[gmx-users] questions on ligand.gro and ligand.itp preparation

[Brett]

Dear All,


Here I have 2 questions related to the ligand.gro and ligand.itp preparation for the md of protein-ligand complex.


First, we have different ways to get the ligand.itp by different serves which use different electronic charge assignment methods. Is any difference for the md result for the whole protein-ligand complex if we use ligand.itp got by different charge assignment methods?


Second, in the Justin on-line tutorial for the md of protein-ligand, it has the method to edit the complex.gro, for example the Justin tutorial final format was:
163ASN      C 1691   0.621  -0.740  -0.126
163ASN     O1 1692   0.624  -0.616  -0.140
163ASN     O2 1693   0.683  -0.703  -0.011
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C14 2 2.392 -2.470 -0.139
1JZ4 C13 3 2.246 -2.441 -0.181
......
5.99500   5.19182   9.66100   0.00000   0.00000  -2.99750   0.00000   0.00000   0.00000


My question is, suppose we have an artificial lysozyme which contains 2 lysozyme subunit, each subunit binding one JZ4, then how do we edit the complex.gro? Does the final complex.gro change into something like?


163ASN      C 1691   0.621  -0.740  -0.126
163ASN     O1 1692   0.624  -0.616  -0.140
163ASN     O2 1693   0.683  -0.703  -0.011
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C14 2 2.392 -2.470 -0.139
1JZ4 C13 3 2.246 -2.441 -0.181
....
2JZ4 C4 (followed by coordinates)
2JZ4 C14 (followed by coordinates)
2JZ4 C13 (followed by coordinates)
5.99500   5.19182   9.66100   0.00000   0.00000  -2.99750   0.00000   0.00000   0.00000


I am looking forward to getting your reply.


Brett