Dear AMBER users,
Seems that the "strip" command was useful for the analysis of each of my
protein chains since I could mask the atoms I was not focused for my
analysis.
The thing is when I am trying to analyze RMSD for the two chains (general
RMSD) my out put is always for one the chains. My protein has two chains
both named as "C" and numbered equally 20-450,
What I have done is for example:
rms 20-450.CA reference out allprot.dat : but with this I
always obtain analysis for just one chain
So my question is how could I indicate in this script that I need the RMSD
analysis for both chains (all the protein) at the same time?
Thanks in advance
2014-04-22 17:50 GMT+02:00 Asaminew Haile <ashaethio.gmail.com>:
>
> 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
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>> _______________________________________________
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> >>> 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 201
> >> Salt Lake City, UT 84112-5820
> >> 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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>
>
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Received on Thu Apr 24 2014 - 02:30:02 PDT
