AMBER Archive (2004)

Subject: Re: AMBER: Improper dihedral

From: Herbert Georg (
Date: Mon Jan 12 2004 - 14:21:39 CST

When I use the saveamberparm command, Leap gives messages like 'Checking
unit', 'Building topology', things like that... and it gives a message
which is '0 impropers applied' or something like this... when I load a
prep file and use saveamberparm, leap gives a message like '5 impropers
used' and it lists the impropers used. Loading a PDB is not working the
same way...

Bill Ross escreveu:

>>In this case the bonds are recognized as I can see with the desc
>>command and xleap shows the bonds between the atoms. The centers are in
>>the 3rd place also. So I don't know why it doesn't apply the impropers.
>>I suppose that, being the center atom in the 3rd place, it doesn't
>>matter the order of the remaining 3 atoms, as it seems not to matter in
>>the case of BONDS and ANGLES.
>It sounds like it should work. How do you know it isn't applying
>I will leave this to the current leap support staff.
>Bill Ross
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