Yeah pretty sure you will have to use the GitHub or the AT21 version.
-Dan
On Thu, May 13, 2021 at 11:06 AM ARITRA MITRA <aritra18.iitg.ac.in> wrote:
> Dear Dan,
> The CPPTRAJ version I am currently using is:
>
> CPPTRAJ: Version V4.14.0 (AmberTools V19.00)
>
>
> Regards,
>
> Aritra Mitra,
>
> Senior Research Fellow,
>
> Prof. Sandip Paul's Group,
>
> Department of Chemistry,
>
> IIT Guwahati.
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: 13 May 2021 20:32
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising
> this issue again.
>
> Hi,
>
> What Version of CPPTRAJ are you using? You may need the latest from GitHub
> for the <= operator to work.
>
> -Dan
>
> On Thu, May 13, 2021 at 10:34 AM ARITRA MITRA <aritra18.iitg.ac.in> wrote:
>
> > Dear Dan,
> > I am following your code but ending up with syntax errors. Here is a
> > sample of the code I am running:
> >
> > set out1 = number_density.dat
> >
> > set del = 'delta 0.1'
> >
> > set mask = '":OLA| :LQZ"'
> >
> > parm des-50-wat-50-253K.prmtop
> >
> > trajin des50-pd-1076ns.nc
> >
> > set MAX = trajinframes
> >
> > clear trajin
> > for i=1;i<=$MAX;i++
> > trajin des50-pd-1076ns.nc $i $i
> > center $mask origin
> > density out ./out_files/$out1.$i number $del $mask name frame.$i
> > clear trajin
> > done
> >
> > The error I am getting is as follows:
> >
> > [for i=1;i<=1000;i++]
> > Setting up 'for' loop.
> > Error: End argument must be an integer.
> > 1 errors encountered reading input.
> > I am not sure as to where I am going wrong. I have looked up the usage of
> > for loops in CPPTRAJ and I can't figure out the error in my code.
> > I am using AmberTools19. Can you please help me out?
> >
> >
> > Regards,
> >
> > Aritra Mitra,
> >
> > Senior Research Fellow,
> >
> > Prof. Sandip Paul's Group,
> >
> > Department of Chemistry,
> >
> > IIT Guwahati.
> >
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: 12 May 2021 00:39
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising
> > this issue again.
> >
> > Hi,
> >
> > You might be able to get what you want with a for loop. Something like:
> >
> > set masks = '":PC.P31" ":PC.N31" ":PC.C2" ":PC | :OL | :OL2"'
> > set del = 'delta 0.25'
> > set out1 = number_density.dat
> > parm ../DOPC.parm7
> > trajin ../DOPC.rst7
> > # Set MAX to the current number of frames
> > set MAX = trajinframes
> > # Clear the trajectory
> > clear trajin
> > # Loop over each frame individually, calculate density
> > for i=1;i<=$MAX;i++
> > # Load only the desired frame
> > trajin ../DOPC.rst7 $i $i
> > center ":PC | :OL | :OL2" origin
> > density out $out1.$i number $del $masks name frame.$i
> > # Clear that frame
> > clear trajin
> > done
> >
> > Hope this helps,
> >
> > -Dan
> >
> > On Tue, May 11, 2021 at 2:03 PM ARITRA MITRA <aritra18.iitg.ac.in>
> wrote:
> > >
> > > Dear Amber Users,
> > > This query is regarding the 'density' analysis in CPPTRAJ. I am running
> > the following script in order to obtain the density distribution of water
> > as a function of box length in the x direction.
> > >
> > > parm abc.prmtop
> > > trajin abc.crd
> > > density out wat-density-x.dat name x-axis-wat delta 0.1 x mass :WAT
> > >
> > > The output file contains the density values averaged over the entire
> > trajectory (along with the standard deviation values) . For the purpose
> of
> > my analysis, I wish to calculate the
> > > density values per frame such that in addition
> > > to the box length and density data the time information will also be
> > written out. I need a workaround to bypass the time average feature of
> the
> > 'density' keyword. Any suggestion on this
> > > topic is highly appreciated.
> > > Thanks in advance.
> > >
> > >
> > >
> > > Regards,
> > >
> > > Aritra Mitra,
> > >
> > > Senior Research Fellow,
> > >
> > > Prof. Sandip Paul's Group,
> > >
> > > Department of Chemistry,
> > >
> > > IIT Guwahati.
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu May 13 2021 - 09:30:02 PDT
