Re: [gmx-users] Salt bridge observation

2013-04-04 Thread Justin Lemkul
On 4/4/13 12:27 AM, Kavyashree M wrote: Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb

Re: [gmx-users] Salt bridge observation

2013-04-04 Thread Kavyashree M
Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Thanks Regards Kavya On Thu, Apr 4, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 12:27 AM,

Re: [gmx-users] Salt bridge observation

2013-04-04 Thread Justin Lemkul
On 4/4/13 4:34 AM, Kavyashree M wrote: Sir, Why I mentioned NH2 CG saltbridge because the g_saltbr gives the charge group and does not mention the OD2 of ASP but mentions only CG. Otherwise it does not make any sense. Now I remember how g_saltbr naming works. It measured distances between

Re: [gmx-users] Salt bridge observation

2013-04-04 Thread Kavyashree M
Ok. Still the distance is beyond the mentioned cut-off. The distance of both OD1 and OD2 of ASP is more than 4 Ang from NH2 of Arg. Thank you Regards Kavya On Thu, Apr 4, 2013 at 2:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/4/13 4:34 AM, Kavyashree M wrote: Sir, Why I mentioned

Re: [gmx-users] Salt bridge observation

2013-04-04 Thread Justin Lemkul
On 4/4/13 5:18 AM, Kavyashree M wrote: Ok. Still the distance is beyond the mentioned cut-off. The distance of both OD1 and OD2 of ASP is more than 4 Ang from NH2 of Arg. The cutoff is applied per group, not per atom within the group, IIRC. So if the charge group at any time comes closer

[gmx-users] Salt bridge observation

2013-04-03 Thread Kavyashree M
Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues

Re: [gmx-users] Salt bridge observation

2013-04-03 Thread Justin Lemkul
On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a

Re: [gmx-users] Salt bridge observation

2013-04-03 Thread Kavyashree M
Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f