Re: Re: [gmx-users] Angle definition in g_hbond ...

] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 5 May 2008 23:13:25 +0530 Subject: Re: [gmx-users] Angle definition in g_hbond ... Hi, Just calculate the no. of atoms according to the choice of options and manually. you will understand why is it giving the error. Secondly

Re: [gmx-users] Angle definition in g_hbond ...

+0530 Subject: Re: [gmx-users] Angle definition in g_hbond ... Hi, Just calculate the no. of atoms according to the choice of options and manually. you will understand why is it giving the error. Secondly check how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm and 30

Re: Re: [gmx-users] Angle definition in g_hbond ...

list for GROMACS users gmx-users@gromacs.org Date: Tue, 06 May 2008 15:03:30 +0200 Subject: Re: [gmx-users] Angle definition in g_hbond ... sharada wrote: Hi, Thank you all for the response, Yes, the backbone of my protien does not have the required -Hydrogens for the program to calculate

[gmx-users] Angle definition in g_hbond ...

dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at all . However, when I plot the hydrogen

Re: [gmx-users] Angle definition in g_hbond ...

sharada wrote: dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at all . However, when I

Re: [gmx-users] Angle definition in g_hbond ...

Mark Abraham wrote: sharada wrote: dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at

Re: [gmx-users] Angle definition in g_hbond ...

Hi, Just calculate the no. of atoms according to the choice of options and manually. you will understand why is it giving the error. Secondly check how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm and 30 in version 3.3.1, but in earlier version the angle cut-off was