Hi,
On Tue, Apr 22, 2014 at 6:12 AM, Asaminew Haile <ashaethio.gmail.com> wrote:
>
> On Apr 22, 2014, at 7:56 AM, Marlet Martinez <marletm8.gmail.com> wrote:
>
>> Dear Amber users,
>>
>> I am training to make some structural analysis in just of the two chains
>> of my protein, since their numbering is exactly the same e.g 1-20 and the
>> both are named as chain "C"
>>
>> So I was wondering if there is a way in amber to strip atoms instead of
>> residues like when executing strip command e.g: strip: 1-20
The atom selection syntax character is '.', so if you want all atoms
named 'OP1' for example you would use the mask '.OP1', etc.
> example
> strip 1-20.H*
I think you meant ':1-20.H*' (without the residue ':' operator this is
an invalid mask). See section 28.2.3 of the Amber14 manual for a more
detailed description of mask selection syntax, including several
examples.
Hope this helps,
-Dan
> will strip all Hydrogen
>
>> (this only
>> works to "mask" residues but not atoms" in order to perform RMSD
>> calculation.
>>
>> Thanks in advance,
>>
>> Best regards
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>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Tue Apr 22 2014 - 07:30:02 PDT
