[AMBER] Possible bug in LEaP with ff12SB

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Thu, 25 Oct 2012 11:23:32 +0000

Hello everyone,
I found a possible bug in LEaP when used with ff12SB. I haven't seen this described anywhere else, and it could be of interest to other people.
My work involves a fair amount of custom residues, so I often have to generate new ones and give parameters to them with LEaP. The way I go about doing this is by using the set command, this way:
> set XXX.N.M parameter object
where XXX is the unit, N the residue, M the atom number, parameter what I need to set (element, atom type, atom name, and so on) and object what I want the parameter to be. The problem arose when I tried to add a residue after upgrading from ff99SB and setting the parameters to the correct values: if I tried to set the element to something as simple as carbon (C), with a command like this,
> set UNIT.1.3 element C
it would not allow me to do so, though nitrogen (N), hydrogen (H), and oxygen (O) all worked without problem; similarly, it wouldn't let me set the type of the carbonyl carbon on the backbone to its correct type (C), while all other types worked. The error is always the same: "The value must be of the type: String". This did not appear with ff99SB.
After some prodding and poking, I figured that the problem happens because the string C is assigned to a premade residue: cytosine. LEaP misinterprets the command and fails to change the element or type to C. This occurs with any prebuilt residue name, from A to WAT, and did not happen in ff99SB because cytosine is named RC, perhaps specifically to avoid this issue.
As I need to set things to C very often, my fix will probably be to rename cytosine back to RC in some way, but I'm open to other workarounds.
I hope this problem can get solved.
Kind regards
Pietro Aronica
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Received on Thu Oct 25 2012 - 04:30:03 PDT
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