[AMBER] problem with AMBER TUTORIAL A1

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Fri, 13 Oct 2017 12:27:12 +0000

Dear Amber experts,

I have on my Linux sever Amber16 and AmberTools16.

I need to MD simulate protein containing non-standard amino-acid residue
that is not parameterized in the leaprc.protein.ff14SB library.

In order to solve the problem I decided to follow the

Simulating a Solvated Protein that Contains Non-Standard Residues
(More Advanced Version) By Ross Walker<mailto:amber_tutorial_query.rosswalker.co.uk>

I have faced the problem of the Table opening where the atomic charges
of the non-standard residue generated previously by RED server should be inserted.
See below the original Tutorial Text in the chapter "Creating MEM and HIC units":

 “For the purposes of this tutorial we will use the charges shown in the screen shot below.
In order to specify the charges and atom types we need to select the entire unit.
Hit the select button in the Manipulation bar and then rubberband the entire molecule.
It should all change colour. Then go to the Edit menu:

Edit->Edit Selected Atoms

The following box should come up with Table. You should now go through and assign
an atom type and charge for all of the atoms.”

The problem is that the desired Table is not opened with the command stated
in the Tutorial above!

I need your expert advice how to resolve the problem of the Table opening in
the xleap graphical window in order to assign the RED atomic charges.

Thank you,

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Received on Fri Oct 13 2017 - 05:30:04 PDT
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