Please upgrade to the github version or the version from ambertools 19.
-Dan
On Thu, May 30, 2019 at 9:23 PM Reber, David <David.Reber.empa.ch> wrote:
> 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 - 18:30:04 PDT
