Re: [AMBER] GIST calculation on NAMD-generated trajectory

From: anthonycruzpr <>
Date: Wed, 12 Dec 2018 18:42:11 -0500

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 (, 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 ( If you decide to use SSTMap we will be happy to help you.
Please, fell free to contact us if you need more help.
Anthony Cruz

Sent from my Sprint Samsung Galaxy S® 6 edge.
-------- Original message --------From: Bin Sun <> Date: 12/11/18 2:52 PM (GMT-05:00) To: 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 ( 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", 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 Wed Dec 12 2018 - 15:00:02 PST
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