Thank you Dan for the clarifications.
Indeed the line you indicated appears in the output.
Regards
George
On 23Feb, 2015, at 3:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Feb 23 2015 - 11:00:05 PST
