Date: Wed, 3 Feb 2016 09:17:53 -0700
Hi,
After running with the files you provided everything seems to be
working fine for me. Using the input and the files you provided like
so:
parm run.prmtop
trajin frame11.mdcrd
strip :158.H*
mask "(:158<:4)&!:158" maskout mask.out maskpdb mask.pdb
distance :158.O .58 out dist_11_58.dat
the generated PDB appears OK (pic attached). The distance you get from
the 'distance' command (7.0195) is indeed larger than 4 Ang, but this
is because you specified you wanted *residues* within 4 Ang, not
*atoms*, so if any part of the residue is within 4 Ang it is selected.
However, I'm not seeing distances up to 34 Ang - the largest I see in
the PDB is 16.158 Ang.
I recommend upgrading to at least the latest AmberTools version of
cpptraj (15) - there have been many fixes since version 14.
Hope this helps,
-Dan
On Tue, Feb 2, 2016 at 8:27 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Can you send me off-list the trajectory frame in question (number 11)
> along with the corresponding topology file so I can try to reproduce
> what you are seeing? Also, what version of cpptraj are you using
> (cpptraj --version)? Thanks.
>
> -Dan
>
> On Tue, Feb 2, 2016 at 2:28 AM, A kS <aks25121986.gmail.com> wrote:
>> Dear AMBER user,
>>
>> I am using *mask command* in *cpptraj of AT14* to:
>>
>> <1> I want to know the *atoms that are within the 4A from the oxygen atom
>> of a water molecule* (WAT.O) (solvent mask :158)* for a particular frame*
>> in an *autoimaged trajectory* as :
>>
>> trajin autoimaged.mdcrd 11 11
>> strip :158.H*
>> mask "(:158<:4)&!:158" maskout mask.out
>>
>> *MY PROBLEM IS*:
>>
>> When I calculate the *distance between the atoms* that are coming out from
>> the mask command and the :158.O for that particular frame as :
>>
>> trajin autoimaged.mdcrd 11 11
>> distance :158.O .58 out dist_11_58.dat
>>
>> *I have found some of the distance >4A even upto 34A.*
>>
>> I think this should not be happens but I am unable to identify the problem.
>>
>> Regards
>> Aks
>> _______________________________________________
>> AMBER mailing list
>> 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/
> (801) 587-9652
> (801) 585-6208 (Fax)
-- ------------------------- 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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(image/jpeg attachment: mask.pdb.1.jpg)
