You want the stand-alone CPPTRAJ, see:
https://github.com/Amber-MD/cpptraj/blob/master/doc/CpptrajDevelopmentGuide.pdf
________________________________________
From: Reber, David <David.Reber.empa.ch>
Sent: Thursday, May 30, 2019 8:17:53 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Radgyr or distance averages
I have copied the amber16 folder into "my" directory where I have write permission, changed $amberhome accordingly and dowloanded the git-cpptraj .zip file.
Could you be so kind to run me through the installation of the new CPPTRAJ?
> -----Original Message-----
> From: Thomas Cheatham [mailto:tec3.utah.edu]
> Sent: Freitag, 31. Mai 2019 04:07
> To: AMBER Mailing List
> Subject: Re: [AMBER] Radgyr or distance averages
>
>
> You probably cannot install in the system branch that your "host" maintains,
> but why not just download CPPTRAJ from the Git page and install in your
> home directory? It is not that big and fairly easy to do....
> ________________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, May 30, 2019 7:39:12 PM
> 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
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
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Received on Thu May 30 2019 - 19:30:03 PDT
