Re: [gmx-users] water in protein itp file

2006-11-14 Thread raja
Dear Mark, Thaks for your replies and I end this discussion with this. B.Nataraj On Wed, 15 Nov 2006 11:51:37 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: > raja wrote: > > Dear Mark, > > Well and thanks again, QM-MM is a good option, as you said for analyzing > > the energetic of water liga

Re: [gmx-users] water in protein itp file

2006-11-14 Thread Mark Abraham
raja wrote: Dear Mark, Well and thanks again, QM-MM is a good option, as you said for analyzing the energetic of water ligating process. But my case not concerning to that process, rather study a system consists of a macromolecule as a whole, where this water bound zinc is a part of it. If this i

Re: [gmx-users] water in protein itp file

2006-11-13 Thread raja
Dear Mark, Well and thanks again, QM-MM is a good option, as you said for analyzing the energetic of water ligating process. But my case not concerning to that process, rather study a system consists of a macromolecule as a whole, where this water bound zinc is a part of it. If this is a case of QM

Re: [gmx-users] water in protein itp file

2006-11-13 Thread Mark Abraham
raja wrote: Dear Mark, Thanks for your immediate reply and good solution. But until before yours this mail, I was thinking that inclusion of water and restraining them with metal ion is a very common happening in MD. Since in my short spell of molecular modeling and drug design experience, I have

Re: [gmx-users] water in protein itp file

2006-11-13 Thread raja
Dear Mark, Thanks for your immediate reply and good solution. But until before yours this mail, I was thinking that inclusion of water and restraining them with metal ion is a very common happening in MD. Since in my short spell of molecular modeling and drug design experience, I have found almost

Re: [gmx-users] water in protein itp file

2006-11-13 Thread Mark Abraham
raja wrote: Dear gmxions, I want to include one crystal water within protein itp, to further restrict it by harmonic bond with metal ion at the active site. In other words, one of the water molecules to be treated just likes another protein residue by pdb2gmx. How to do that? Nobody here owes

[gmx-users] water in protein itp file

2006-11-13 Thread raja
Dear gmxions, I want to include one crystal water within protein itp, to further restrict it by harmonic bond with metal ion at the active site. In other words, one of the water molecules to be treated just likes another protein residue by pdb2gmx. How to do that? My earlier posting on the same t