Re: [AMBER] MM-PBSA atom types

From: Jason Swails <>
Date: Tue, 4 Aug 2015 12:09:18 -0400

On Tue, Aug 4, 2015 at 11:40 AM, bharat lakhani <>

> So finally I was able to figure out what changes needed to make in
> mdread2.F90 for O3 atom type as following
> else if (atype == 'O3') then
> x(l165-1+i) = 1.60d0 + 1.4d0
> x(l170-1+i) = 0.0d0
> x(l175-1+i) = 0.0d0
> x(l180-1+i) = 0.0d0
> x(l185-1+i) = 0.0d0
> I have recompiled by doing make install but Still the same problems
> persist. Please let me know

​I personally don't see how this error is possible for AmberTools 15 with
an oxygen atom.​ The place you made this change *cannot* hit this fatal
error message as far as I can tell, and the only place where this error
message is actually printed has code there to support oxygen atoms.

Can you send me your topology files and the first couple frames of your
trajectory along with the input file so I can try and reproduce


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 04 2015 - 09:30:03 PDT
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