Thank you very much Dan. The “nointramol” flag confused me a bit. Is it strictly necessary when one defines masked residues?
How could the script be modified to identify bonds ONLY between the ligand(s) in the mask and ANY protein residues or Water molecules?
I tried:
hbond H1 :126,252 series out Nhbond.agr avgout avg.dat bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
It only produced h-bonds with the solvent.
Regards
George
> On 7Mar, 2015, at 7:38 PM, Daniel Roe <daniel.r.roe.gmail.com <mailto:daniel.r.roe.gmail.com>> wrote:
>
> Hi,
>
>
> On Fri, Mar 6, 2015 at 10:44 AM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>> My question is why does the script above (ligand mask included) produce h-bonds with the solvent only but now with Trp114, Phe123 and Trp240?
>
> I think the Amber 14 manual has a decent description of how the atom
> masks work in the cpptraj hbond command. In the first case (where the
> mask :126,252 is given) you restrict your donor/acceptor search to
> those two residues, and consequently obtain only hydrogen bonds
> including those two residues. If you don't specify a mask (your second
> case), as stated in the manual:
>
> "all solute atoms if no mask specified"
>
> which is why you get more hydrogen bonds.
>
> Hope this helps,
>
> -Dan
>
>>
>> Thank you in advance for any comments/suggestions
>>
>> 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/ <http://home.chpc.utah.edu/~cheatham/>
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>
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Received on Sat Mar 07 2015 - 15:30:02 PST
