Hi,
The only thing that seems odd to me is that this line should appear in both
instances:
DE4_127.O1 SolventH SolventDnr 214 0.0214
2.7486 158.8356
but it is missing from the first instance. Since you wrote "(indicative few
lines):", maybe you forgot to paste it in the first instance? Otherwise the
behavior is entirely consistent with what is explained in the manual:
"Search solute for hydrogen bond donor and acceptor atoms in the region
specified by <mask> (all solute atoms if no mask specified)..."
Since in the second instance you specify ":126-127" and "nointramol" the
only hydrogen bonds that will be detected are intramolecular hydrogen bonds
(or solute-solvent bridges) involving residues 126, 127 and solvent.
Hope this helps,
-Dan
On Mon, Feb 23, 2015 at 11:12 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Using the following script
>
> parm 3n7h_de4_solv.prmtop
> trajin prod_100ns.nc
> hbond H1 nointramol series out Nhbond.agr avgout avg.dat
> \ bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
> go
> write solutehb.agr H1[solutehb]
> runanalysis lifetime H1[solutehb] out lifehb.agr window 10
>
> produces the expected output e.g.
>
> the avg. dat file (indicative few lines):
> #Acceptor DonorH Donor Frames Frac
> AvgDist AvgAng
> DE4_127.O1 SER_79.HG SER_79.OG 122 0.0122
> 2.7246 162.2751
> DE4_127.O1 HIE_111.HE2 HIE_111.NE2 10 0.0010
> 2.8810 152.6329
> DE3_126.OAN TRP_114.HE1 TRP_114.NE1 1 0.0001
> 2.8386 174.1757
> #Solute-Solvent Hbonds:
> #Acceptor DonorH Donor Count Frac
> AvgDist AvgAng
> DE3_126.OAN SolventH SolventDnr 8643 0.8643
> 2.7484 163.2506
>
> the bridge.dat file
> #Bridging Solute Residues:
> Bridge Res 95:CYX 114:TRP 126:DE3 , 3555 frames.
> Bridge Res 114:TRP 126:DE3 , 2006 frames.
> Bridge Res 95:CYX 126:DE3 , 1823 frames.
>
> Changing the input line of the script by using a mask (residues 126 and
> 127 are ligands)
> hbond H1 :126-127 nointramol series out Nhbond.agr avgout avg.dat
> \ bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
>
> produces a similar but non-identical output for agv.dat
> #Acceptor DonorH Donor Frames Frac
> AvgDist AvgAng
> #Solute-Solvent Hbonds:
> #Acceptor DonorH Donor Count Frac
> AvgDist AvgAng
> DE3_126.OAN SolventH SolventDnr 8643 0.8643
> 2.7484 163.2506
> DE4_127.O1 SolventH SolventDnr 214 0.0214
> 2.7486 158.8356
>
> and no bridge H-bonds
> #Bridging Solute Residues:
>
> I’d be grateful for any explantation of this behavior
>
> Regards
>
> George
>
>
>
>
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Feb 23 2015 - 11:00:03 PST
