Re: [AMBER-Developers] significant recent tleap changes

From: Yong Duan <>
Date: Fri, 11 Nov 2011 14:15:12 -0800

Improper 1-4's are never used, either in sander or in pmemd. I am not sure
in other programs, hopefully consistent. Putting 0's is fine. I can update

The IPOL is a new addition. If you refer to the warning message, it is
designed to warn the users that mixing polarizable and non-polarizable
force fields is not a good idea. If you refer to the prmtop, this is a new
feature of prmtop. Sander (and soon PMEMD) will take ipol from prmtop, not
from mdin. It does not make sense to let users have the freedom to mix
different models and expect physically/chemically sound results.

Besides these "failures", you will also see CMAP-related failures. Both
sander and pmemd can take CMAP without CHARMM option.

This means the test suite needs to be updated and that the "new" test
suite will cause a lot of "failures" to the old code and vice versa.


On 11/11/11 1:18 PM, "David A Case" <> wrote:

>On Fri, Nov 11, 2011, Jason Swails wrote:
>> ....deficient tleap test suite. The current tests
>> ($AMBERHOME/AmberTools/test/leap) only test the creation of OFF library
>> files and old-style topology files(!)
>Wow...I had forgotten that the "set default OldPrmtopFormat on" command
>> The behavior we discussed in
>> is no more (impropers no
>> longer get 0's, they get 1.2/2.0).
>> Do we want to go back to the original behavior (which would require
>> some of Arunima's original code back in) or just live with the new
>I think we want to go back to the original idea, with 0's.
>AMBER-Developers mailing list

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Received on Fri Nov 11 2011 - 14:30:02 PST
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