[AMBER] GIST calculation on NAMD-generated trajectory

From: Bin Sun <sunbinhrx.gmail.com>
Date: Tue, 11 Dec 2018 14:52:48 -0500

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

Thanks very much!

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Received on Tue Dec 11 2018 - 12:00:02 PST
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