Hi,
On Sat, Mar 7, 2015 at 4:12 PM, George Tzotzos <gtzotzos.me.com> wrote:
> 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?
The 'nointramol' keyword tells cpptraj to ignore hydrogen bonds that
are between atoms in the same molecule. So by adding 'nointramol' to
your command you should only get hydrogen bonds between ligand-solute,
ligand-water, and solute-water. If you don't want solute-water you
will need to use two commands:
# For solute-ligand
hbond H1-U-L series out Nhbond.agr nointramol avgout avg.U-L.dat
# For ligand-solvent
hbond H1-L-V series out Nhbond.agr :126,252 avgout avg-L-V.dat
bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
Hope this helps,
-Dan
>
> 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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>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> 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/ <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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> 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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Received on Mon Mar 09 2015 - 07:30:11 PDT
