Bin,
As Dan replied, it is our understanding that GIST in cpptraj should work
regardless of the trajectory format and forcefield (i.e. it should work for
your simulation) with AmberTools18. I was hoping you could install the
current version to AmberTools18 and then test with your system.
Best,
Tom
************************************************
Tom Kurtzman, Ph.D.
Associate Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<
http://www.lehman.edu/faculty/tkurtzman/index.html>
************************************************
On Thu, Dec 13, 2018 at 2:59 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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--
************************************************
Tom Kurtzman, Ph.D.
Associate Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<http://www.lehman.edu/faculty/tkurtzman/index.html>
************************************************
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Received on Tue Dec 18 2018 - 10:30:03 PST
