Re: Amber on with H-bond

From: Fangqiang Zhu (
Date: Wed Mar 03 2004 - 21:45:15 CST


In some old Amber force fields, there's a 10-12 potential term (probably
for explicit hydrogen bond energy) in addition to the normal 6-12
potential. NAMD doesn't support such 10-12 potential, and will complain and
terminate if it finds a non-trivial 10-12 term in the parm file. However, for
reasons which I don't know, some new Amber parm files also contain one 10-12
parameter, but with a zero energy constant; in this case NAMD will simply
ignore that term and continue after giving a warning. That's the reason for
first warning.

The second warning (about H-H bonds) is most often caused by water
molecules, because in some water models there's a bond connecting the two
hydrogen atoms of a water molecule.

None of these two warnings should affect the correctness of the simulation.

Zhu, Fangqiang

Sichun Yang wrote:

> Dear All,
> I run the simulaiton with AMBER on.
> But in the output, I found the warning message.
> Reading parm file (new.prmtop) ...
> PARM file in AMBER 7 format
> Warning: Encounter 10-12 H-bond term
> Warning: Found 4879 H-H bonds.
> What does this mean? Any hint?
> In the manual, it says NAMD might terminate when not-zero 10-12 papameters
> are there in PARM file. However, NAMD continues to run in my case.
> So what happened?
> Thanks,
> Sichun

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