Re: [AMBER] Problem with idecomp in MMPBSA

From: Jason Swails <>
Date: Thu, 15 Jan 2015 10:52:28 -0500

On Thu, 2015-01-15 at 12:01 -0300, wrote:

> I found in previous messages that it was neccesary to modified the mdread
> file in sander adding these lines:
> else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe') then

This will never work, because atype(1:1) is a single character so it
cannot possibly match a 2-letter string. Perhaps you meant atype(1:2)?

> x(l165-1+i) = 0.78d0 + 1.4d0
> x(l170-1+i) = 0.00000d0
> x(l175-1+i) = -0.00000d0
> x(l180-1+i) = -0.00000d0
> x(l185-1+i) = 0.00000d0
> and reinstalling but I have already done this without success.
> Any ideas of how overcome this problem?

This doesn't look quite like the right code to add for Amber 14. Amber
14 assigns these parameters by atomic number now -- not the atom type
string. The change I suggested above might work, but it would be better
IMO to change it to something like:

else if (atomicnumber == 26) then
   x(l165-1+i) = 0.78d0 + 1.4d0

You may also want to consider changing the "else" clause to assign some
"default" parameter (maybe 1.7 -- the value for carbon) and emit a
warning. At the end of the day, these parameters are just used for the
SASA calculation. Having only one or two atoms assigned a radius that
is off even by an angstrom or two will probably have a negligible effect
on the total SASA (most likely well within the uncertainty of the SASA
calculation itself). For qualitative comparisons (which is really all
decomposition calculations are good for), it should be fine.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 15 2015 - 08:00:05 PST
Custom Search