Ok, I am contacting my host, I don't have permission to execute the commands you suggested. Is it possible to just update cpptraj while still using Amber16 or is an update to Amber18 required as well?
Thank you very much for your help
David
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Freitag, 31. Mai 2019 03:39
> To: AMBER Mailing List
> Subject: Re: [AMBER] Radgyr or distance averages
>
> Unfortunately no. The 'for' syntax is pretty recent - I think you'll
> need at least the AmberTools 18 version.
>
> If you have access to compilers, you could try compiling yourself. If
> the rest of amber is available (and you have access to compilers) it's
> fairly simple: with AMBERHOME set just './configure -amberlib gnu'
> followed by 'make install' to build the latest cpptraj.
>
> -Dan
>
> On Thu, May 30, 2019 at 9:33 PM Reber, David <David.Reber.empa.ch>
> wrote:
> >
> > 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 - 19:00:04 PDT
