Hi anthonycruzpr,
Thanks for your kind reply. I have successfully used the SSTMap program
which solved my problem.
Best,
Bin
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.
> 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
