On Apr 22, 2014, at 11:43 AM, Marlet Martinez <marletm8.gmail.com> wrote:
> Dear all,
>
> Thanks for your kind response
>
> Actually what I was trying to do was to "mask" or "strip" some atoms that
> correspond to several residues of one of the chains of my protein. So I
> was wondering If I should do: strip .1-500 in order to mask all the
> atoms that belong for the chain that has 500 residues (1-500) is that
> correct?
here is my actual input for similar reasons
cat <<EOF >rms. in
reference reference.pdb
trajin trajectory.netcdf
rms reference mass out name.rms :1-500.!H=
EOF
ptraj name.prmtop <rms.in
this will find the RMSD of all heavy atoms in residue 1-500
>
> I guess for RMSD, RMSF I should use the same instruction if I want to mask
> those atoms , right?
>
> Thank you so much for your suggestions
>
>
>
>
> 2014-04-22 16:10 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> 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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>>
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Received on Tue Apr 22 2014 - 09:00:04 PDT
