[AMBER] Ca ion bond distances restraints with chelator ?

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Thu, 25 Oct 2018 12:25:35 +0000

Dear AMBER Experts,

I need to simulate by molecular dynamics
protein-ligand complex.
I use AMBER16 and AMBER TOOLS16.
The small molecule ligand (MOL) chelates Ca(2+) cation.
Ca forms 6 bonds with chelator oxygen atoms.
In order to prevent the Ca ion release to the solvent during MD simulation
I decided to use bond restraints algorithm implemented in AMBER.

I have generate 7-column 7col.dist file:
349 CA CA 1 MOL O1 2.4
349 CA CA 1 MOL O4 2.4
349 CA CA 1 MOL O5 2.7
349 CA CA 1 MOL O6 2.7
349 CA CA 1 MOL O8 2.4
349 CA CA 1 MOL O9 2.4

Then I ran the makeDIST_RST program:
makeDIST_RST -upb 7col.dist -pdb mc_min1.pdb -rst RST.dist

Unfortunately, AMBER reported error:
# makeDIST_RST
Currently configured for up to 50000 atoms
Using MAP file /var/spool/scratch/shokhen/amber16/dat/map.DG-AMBER
ERROR no map function for CA CA :data= 349 CA CA 1 MOL O1 2.4

Indeed the map.DG-AMBER file does not contain Ca parameters,
But it contains data for ZN. I tried to add the data for CA by analogy.
Nevertheless AMBER reported error message again.

Do somebody know how to work around the problem and add CA to the
parameters by the way relevant for the makeDIST_RST program?

Thank you,

Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Thu Oct 25 2018 - 05:30:02 PDT
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