Hi,
The keyword is ‘inmask’ (all one word - see the manual or type ‘help for’
for syntax). Also, what version of cpptraj are you using?
-Dan
On Thu, May 30, 2019 at 8:32 PM Reber, David <David.Reber.empa.ch> wrote:
> Hi Dan
>
> I see, thank you for clarification. I tried your suggestion and I get some
> invalid command error messages:
>
> [trajin MD333.mdcrd]
> Reading 'MD333.mdcrd' as Amber Trajectory
> [for residues R0 in mask :FSI i=1;i++]
> Error: Unrecognized character in expression: :
> 'for residues R0 in mask :FSI i=1;i++': Invalid command or expression.
> 1 errors encountered reading input.
>
> Do you see where the problem lies?
>
> Thanks for your help,
> David
>
>
> > -----Original Message-----
> > From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> > Sent: Donnerstag, 30. Mai 2019 17:03
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Radgyr or distance averages
> >
> > Hi,
> >
> > On Wed, May 29, 2019 at 11:24 PM Reber, David <David.Reber.empa.ch>
> > wrote:
> > > If I calculate the radius of gyration or atom-atom distances for one
> > particular molecule in my trajectory I obtain values I would expect.
> > > e.g. my 9-atom anion called FSI(resid 1) "radgyr :1 out ***.dat mass
> > tensor" yields something like 1.9 Angstrom.
> > > If I select all the molecules of a certain type I get values that are
> > approximately half the box size:
> > > "radgyr :FSI out ***.dat mass tensor" yields ca. 20 Angstrom.
> >
> > So as you are seeing, by default the atom masks in these commands
> > apply to all atoms. That is, something like :WAT for 'radgyr' will
> > calculate the radius of gyration of *all* water molecules in your
> > system. So what you would need to do is create a loop over whatever
> > molecules/residues, then calculate the average. So something like this
> > should work:
> >
> > parm myparm.parm7
> > trajin mytraj.nc
> > for residues R0 inmask :FSI i=1;i++
> > radgyr rg$i $R0
> > done
> > avg oversets rg* name AvgRg out AvgRg.dat
> > run
> >
> > If you want the individual radius of gyration values for each residue,
> > just add 'out rg.dat' or something to the 'radgyr' command. Hope this
> > helps,
> >
> > -Dan
> >
> >
> > >
> > > I have the same issue with the distance command. If I select two atoms
> on
> > resid 1 I get reasonable values in the range of 3-4 Angstrom:
> > > "distance :1.F1 :1.F2 out distance.dat"
> > >
> > > if I select all FSI-residues, I get values of about 0.2 A:
> > > "distance :FSI.F1 :FSI.F2 out distance.dat"
> > >
> > > In case of the distance command I assume intermolecular distances are
> also
> > calculated which in the end cancel each other out resulting in the value
> close
> > to zero?
> > >
> > > How can I get the average radgyr or intramolecular atom-atom distances
> > for a certain type of molecule averaged over the whole trajectory?
> > >
> > > Thank you in advance for any hints,
> > >
> > > David
> > >
> > >
> > >
> > >
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Received on Thu May 30 2019 - 18:30:02 PDT
