Hi Dan
Is there a way around updating? I'm just on an exchange where I'm working at the moment and don't have the rights to update anything.
David
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Freitag, 31. Mai 2019 03:29
> To: AMBER Mailing List
> Subject: Re: [AMBER] Radgyr or distance averages
>
> 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 - 19:00:02 PDT
