Same input files. Never needed quotes before. Will run many more tests tomorrow. I did use parallel make for the first time ever, for example. BTW, it worked for 4 & 8 procs, but failed for 16. Will attempt to reproduce.
It DID work, without quotes, for the carbohydrate tests I tried.
Sent from my iPhone
On Mar 19, 2012, at 10:34 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 - 20:30:03 PDT
