Hi Dan
With "inmask" in one word I get the same error. I'm using Version V17.00.
Reading 'MD333.mdcrd' as Amber Trajectory
[for residues R0 inmask :FSI i=1;i++]
Error: Unrecognized character in expression: :
'for residues R0 inmask :FSI i=1;i++': Invalid command or expression.
1 errors encountered reading input.
In the Amber16 manual I cannot find the "inmask" keyword....
David
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Freitag, 31. Mai 2019 03:15
> To: AMBER Mailing List
> Subject: Re: [AMBER] Radgyr or distance averages
>
> 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 - 18:30:03 PDT
