On Tue, Mar 20, 2012, B. Lachele Foley wrote:
>
> source leaprc.ff12SB
> m6 = sequence { NALA ALA ALA CALA }
> impose m6 { 1 2 3 4 } { { N C CA O 120.0 } }
Are there typos here? CA and O are not bonded to each other...
But I can reproduce generally the problems you mentioned. I think it may
not be LEaP that is at fault, but leaprc.ff12SB (or leaprc.ff10). If I go
back to leaprc.ff99SB, things work as expected.
Lachele: it was hard to parse your earlier email: are you seeing (or not
seeing) problems with carbohydrates? Can you see if using leaprc.ff99SB makes
a difference for you? Is there a chance that on Feb. 6 you were using a
different leaprc file?
After a bit of poking around, the problem is that the "C" atom in Lachele's
examples are getting mixed up in LEaP because "C" is also a UnitID (cytosine
in RNA). LEaP expects the arguments to impose to be strings, and stops with
an error message when it finds something that is supposed to be a unit.
The correct(!) way to use the impose command is to force arguments to
be strings:
> m6 = sequence { NALA ALA ALA CALA }
> impose m6 { 3 } { { "N" "C" "CA" "O" 120.0 } }
We should really do this in the examples, and (presumably) in the LEaP
scripts that are running in the background behind the carbohydrate builder
web site.
Also, the error message should be more informative....we had seen this problem
before, but I forgot about it, and it took 45 minutes of poking around before
I remembered what was going on.
(I've now updated the AmberTools12 manual..It's too late to work on better
error messages in LEaP.)
Of course, let us know if this is not the problem, or the whole problem....
....dac
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Received on Mon Mar 19 2012 - 20:00:03 PDT
