AMBER: implicit solvent simulations with calcium ion

From: Akansha Saxena <>
Date: Mon, 10 Dec 2007 13:19:01 -0800 (PST)

Dear Amber users,

I am trying to run an implicit solvent simulation (AMBER8) on a protein bound to a Calcium ion, but I face difficulty in keeping the ion bound to the protein.
The ion moves away from the protein as soon as the production run starts.

To input the non bonded parameters for calcium, I generate the frcmod file:
\# First line; parameters for Ca++.
CAA 40.08

CAA 1.3264 0.44966

The FF used here was parm99.dat. I order to verify that the ion is taking in the correct radii, I spit out the radii information using the trajout -dumpq command of ptraj.
I get a value of 1.9080 for the radius of calcium ion which is very different from what I input.

In order to check if my method is correct I run a similar simulation on a Magnesium bound protein.
Being consistent with my method I generate the frcmod file for Mg as well:
\# First line; parameters for Mg++.
MGG 24.305

MGG 0.78687 0.875119

This time when I output the radii information using trajout -dumpq command of ptraj, I get a value of 0.7869 for Mg ion radius, which is similar to what I input in my frcmod file.

I have two questions:
1) Can somebody tell me why the radius of calcium ion is increased to such a high value. I would think that the failure of my simulations are attributed to the high radii of the calcium ion being used in the calculations because my Mg simulations, where the radius remains the same, run perfectly fine.
2) What radii does trajout -dumpq spits out? The manual says its the RADII flag of prmtop file. This doesn't seem to correspond because if I manually check the RADII flag in the prmtop files of both Mg and Ca simulations, I see a value of 1.5 for both.




Looking for last minute shopping deals?
Find them fast with Yahoo! Search.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Dec 12 2007 - 06:07:22 PST
Custom Search