Re: [AMBER] LEaP failing after update to AmberTools17

From: David Case <>
Date: Wed, 3 May 2017 14:18:10 -0400

On Wed, May 03, 2017, Charles-Alexandre Mattelaer wrote:
> Ever since updating to AT17, Leap is experiencing troubles with generating
> my parameter files. The error that is being produced states:
> > saveAmberParm foo TTT.prmtop TTT.inpcrd
> For atom: .R<DT5 1>.A<HO5' 1> Could not find vdW (or other) parameters for
> type: HO
> ...
> #!/bin/sh
> cat << eof >
> logfile
> source leaprc.DNA.OL15
> foo = sequence {DT5 DT DT3}
> savePdb foo TTT.pdb
> saveAmberParm foo TTT.prmtop TTT.inpcrd
> quit
> eof

I can't reproduce the problem: the above script works for me, with no errors.

So, we will need some more information:

1. How did you get AT17? e.g. via "update_amber --upgrade"? by downloading
    the tar file from the web site? In the latter case, did you un-tar
    the file on top of an existing AT16 distribution?

2. What OS, compiler?

3. Double check that "which tleap" returns what you expect; that AMBERHOME
is correctly defined, etc. But I'm grasping at straws here, as you can tell.
If you have access to another computer with AT16 or AT17 installed, you
could see if you get the same failure there. It might be worth doing a
fresh install of AT17 into a new, pristine directory. Or maybe someone on the
list will recognize the symptoms here.

You could try to narrow down the source of the error: if you use
leaprc.DNA.bsc1 is there a different result? How about trying to make a short

...good luck...dac

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Received on Wed May 03 2017 - 11:30:02 PDT
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