Hi,
The "hbond" command in cpptraj is at the moment a much simpler version
than the one found in ptraj and is designed to quickly provide
information on hydrogen bonds in the region specified by "mask".
Unlike ptraj, cpptraj does not use "donor" or "acceptor" commands to
define hydrogen bonds; instead, it searches the mask region for all
potential donors and acceptors (currently following the simplistic
criterion that "hydrogen bonds are FON", i.e. only hydrogens bound to
F, O, and N are considered). If you want to be able to specify which
atoms to study for hydrogen bonding you currently need to use ptraj.
So, to answer your original questions first:
> 1/ hbond between resid1-resid1
hbond out NHB-residue1.dat :1 avgout AvgHB-residue1.dat
> 2/ hbond between resid1-resid2
hbond out NHB-r1r2.dat :1,2 avgout AvgHB-r1r2.dat
Unfortuntaely in this case there is no way in cpptraj to not look at
hbonds between res1-res1 and res2-res2 since the search for donors and
acceptors is automatic.
> 2/ hbond between resid1-water
Unfortunately not yet implemented in cpptraj (since each water
molecule will currently be considered a separate residue); handling of
solvent Hbonds will be present in the next release of cpptraj. For now
you should just use ptraj for studying solvent-solute hbonds.
-Dan
On Sat, Aug 20, 2011 at 7:16 PM, mirage . <m.o.m.live.fr> wrote:
>
>
>
>> From: m.o.m.live.fr
>> To: amber.ambermd.org
>> Date: Sat, 20 Aug 2011 17:50:12 +0000
>> Subject: Re: [AMBER] hbond atom mask in cpptraj
>>
>> >
>> >
>> > Hi Amber users,
>> >
>> > I want to count hbond with cpptaraj.
>
>
>> > 1/ hbond between resid1-resid1
>
> i do this by "donnor :1" (= or "acceptor :1")
>
>> > 2/ hbond between resid1-resid2
>
> if i do" donnor :1,:2" or "acceptor :1,:2" in the result i found: (hbond resid1-resid1)+ (hbond resid2-resid2)+ (hbond resid1-resid2)
> How to exclude the inter-hbond (hbond resid1-resid1)+ (hbond resid2-resid2)
>
> I want to count just the intermolucular hbond between residu
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Received on Mon Aug 22 2011 - 09:00:04 PDT
