Re: amber-developers: Problem with SHAKE when icfe != 0

From: David A. Case <>
Date: Sun, 19 Mar 2006 23:40:33 -0700

On Sun, Mar 19, 2006, Ilyas Yildirim wrote:

> I have changed the dummy atom type from DH to HA, H and HZ (also HD).
> HA and H, both threads gave the same results. For HZ and HD, it gave
> different results, and the system blows up at the end. I use the same
> extra.frcmod file (except changing the atom type). Here is the .frcmod
> file I am using (the first parts which has the bond info.s in it):
> -----------------------------------------------------
> HZ 1.008
> O -HZ 434.0 1.010 [N2-H]
> CA-N* 424.0 1.383 [C-N*]
> .
> .
> .
> -----------------------------------------------------
> Originally, it was
> O -DH 434.0 1.010 [N2-H]
> I have changed this atom type to H, HA, HZ, and HD.
> I think that SHAKE is turning on the SHAKE constraints of specific
> hydrogen types, not all H-types. I would like to know if this is true.

(a) Use the code, Luke! I'm serious: you need to gain confidence in your
*own* ability to answer questions like these by examining the code to
understand how it works. Often, all you need is some extra print
to give more detailed information.

(b) My guess: you don't mention anything about what "addAtomTypes"
you are giving to LEaP. The leaprc.ff99 file defines HA and H as element
but says nothing about HZ and HD. So, if you used this leaprc, and didn't
additional work, it probalby doesn't think HZ is hydrogen (what is HZ,
anyway?) It's the element that is key, not the mass, or the name, or
else. You have to make sure that LEaP knows about the atom types you are
using, and associates them correctly with elements.

Received on Wed Apr 05 2006 - 23:49:36 PDT
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