Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-31 Thread bharat gupta
I think I answered almost whatever u asked .. I simulated the structure in which the chromophore is not there but its constituent residues are there i.e. ser 65, tyr 66 and gly 67 .. it means that there is no void in the structure .. As I told u in my last mail also that I checked the structure

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-31 Thread bharat gupta
I think I answered almost whatever u asked .. I simulated the structure in which the chromophore is not there but its constituent residues are there i.e. ser 65, tyr 66 and gly 67 .. it means that there is no void in the structure .. As I told u in my last mail also that I checked the structure

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-31 Thread Mark Abraham
On 01/31/11, bharat gupta wrote: > I selected the water molecules but using atom selection in VMD by using the > following command  "water and within 5 of resid 65 to 67", 65 to 67 is the > chromophore position ... some 2 or 3 water molecules were found near to the > chromophore i.e. inside

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-31 Thread bharat gupta
I selected the water molecules but using atom selection in VMD by using the following command "water and within 5 of resid 65 to 67", 65 to 67 is the chromophore position ... some 2 or 3 water molecules were found near to the chromophore i.e. inside the beta barrel ... Practically it should not ha

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-30 Thread bharat gupta
I selected the water molecules but using atom selection in VMD by using the following command "water and within 5 of resid 65 to 67", 65 to 67 is the chromophore position ... some 2 or 3 water molecules were found near to the chromophore i.e. inside the beta barrel ... Practically it should not ha

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-30 Thread Mark Abraham
On 01/31/11, bharat gupta wrote: > I followed the lysozyme tutorial step by step and everything seems to be fine > and the literature cannot be wrong as it has been proved .. > Is your model of the chromophore reasonable? IIRC forming the chromophore requires making some new bonds. > I ha

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-30 Thread bharat gupta
I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it me

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-30 Thread bharat gupta
I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it me

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-30 Thread Mark Abraham
On 01/31/11, bharat gupta wrote: > > > -- Forwarded message -- > From: bharat gupta > > Date: Sun, Jan 30, 2011 at 9:30 PM > Subject: Re: [gmx-users] Monitoring the water movement during simulation > To: Discussion list for GROMACS users > > > > I tracked the movement of

Fwd: [gmx-users] Monitoring the water movement during simulation

2011-01-30 Thread bharat gupta
-- Forwarded message -- From: bharat gupta Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crys