Glad you were able to resolve your issue.
You may want to consider upgrading to AmberTools 18. There have been
many fixes and enhancements since 16.
-Dan
On Thu, Dec 13, 2018 at 2:55 PM Bin Sun <sunbinhrx.gmail.com> wrote:
>
> Hi Dan,
> Thanks for your reply. I was using amber 16 CPPTRAJ.
> Actually, this version of CPPTRAJ indeed can currectly read in psf/dcd
> files and perform analysis
> such as RMSD/RMSF calculations.
> I think it is just the GIST command in CPPTRAJ can only process amber
> generated trajectories..
>
> Best,
> Bin
>
> On Wed, Dec 12, 2018 at 8:40 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Wed, Dec 12, 2018 at 5:43 PM anthonycruzpr <anthonycruzpr.gmail.com>
> > wrote:
> >
> > > Dear Bin:
> > > I can suggest two possible solutions.
> > > 1) The AMBER solution will be to change the CHARMM topology and psf to an
> > > AMBER topology and coordinate by using the chamber option in parmed.
> >
> >
> > This is actually unnecessary as cpptraj can read psf/dcd files natively. I
> > just want to make sure the version of cpptraj being used is up to date.
> > It’s possible that an older version could have some bugs that were fixed in
> > the latest version.
> >
> > -Dan
> >
> >
> > > Unfortunately, I dont have experience doing the change in topology but Im
> > > sure that other user could help you.
> > > 2) Use SSTMap (sstmap.org), a python package that can perform the GIST
> > > analysis and is independent of the simulation package used to generate
> > the
> > > trajectory.
> > > SSTMap was developed by the Kurtzman Lab (
> > > http://www.lehman.edu/faculty/tkurtzman/) If you decide to use SSTMap we
> > > will be happy to help you.
> > > Please, fell free to contact us if you need more help.
> > > Regards,
> > > Anthony Cruz
> > >
> > >
> > > Sent from my Sprint Samsung Galaxy S® 6 edge.
> > > -------- Original message --------From: Bin Sun <sunbinhrx.gmail.com>
> > > Date: 12/11/18 2:52 PM (GMT-05:00) To: amber.ambermd.org Subject:
> > > [AMBER] GIST calculation on NAMD-generated trajectory
> > > Dear amber users,
> > > I want to use the GIST command in CPPTRAJ to calculate the thermodynamic
> > > properties of TIP3P waters around a protein.
> > >
> > > The input trajectory for the calculation is generated by NAMD with
> > CHARMM36
> > > force field, e.g., I have test.dcd and test.psf available. My input file
> > (
> > > gist.in) for CPPTRAJ is as follows:
> > > =========
> > > trajin test.dcd 1 -1 40
> > > gist gridspacn 0.5 gridcntr 9.074 -21.641 11.234 griddim 40 40 40
> > > ==========
> > > after running the command "cpptraj -p test.psf -i gist.in", there is a
> > > error message just saying "segmentation fault".
> > > My guess for the failure is that the GIST command needs correct fore
> > field
> > > parameters to calculate solute-water interaction energies while CPPTRAJ
> > > could not read the CHARMM force filed parameter correctly.
> > >
> > > Is this the reason for the failure of calculation ? Could anyone suggest
> > a
> > > workaround?
> > >
> > > Thanks very much!
> > >
> > > Best,
> > > Bin
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Received on Thu Dec 13 2018 - 12:00:03 PST
