[AMBER-Developers] Program xyz not in amber anymore

From: Hai Nguyen <nhai.qn.gmail.com>
Date: Fri, 06 Oct 2017 22:38:06 +0000

Hi all

We have been seeing similar emails from users.
I think we should not silently turn off the program and hope user to read
1000 page manual.

I think the typical way is to make dummy program and tell user to use the
alternative program (parmed in this case).


---------- Forwarded message ---------
From: Sundar <jubilantsundar.gmail.com>
Date: Fri, Oct 6, 2017 at 6:02 PM
Subject: [AMBER] chamber is unavailable from terminal MacOS
To: <amber.ambermd.org>

Dear Amber community,

I am trying to use AMBER's MMPBSA capability. I have a NAMD dcd and would
like to use it in calculating receptor-ligand binding free energy.

To do that, I installed AmberTools17 and was trying to call in 'chamber'
program to convert CHARMM topologies to Amber topology files. I am unable
to call chamber from terminal in my Mac OS. Other tools like pdb4amber etc.
are there from terminal. Does chamber is not present in $AMBERHOME?

Help me find and run the program successfully. Also let me know if MMPBSA
reads in dcd files with no issues.

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Received on Fri Oct 06 2017 - 16:00:04 PDT
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