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
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,
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
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
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
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
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
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
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