Re: [AMBER] LEaP failing after update to AmberTools17

From: Charles-Alexandre Mattelaer <>
Date: Wed, 3 May 2017 20:39:08 +0200

Thanks for your fast reply.

I'm also grasping at straws and therefor tried the mailing list.

1) I used update-amber --upgrade. This did install the new ambertools in de
amber16 directory, however all the rest is working correctly (or at leasts
seems to be).

2) OS is ubuntu 16.04. I compile using gnu, according to the manual.

3) which tleap outputs the expected directory. I have a working copy of
AmberTools16 on another workstation, on which tleap functions as it should
(scripts runs indeed without error).

I'll give running with other force field parameter files/amino acids a try.
But I'm also under the impression a fresh install shall be necessary if I
can't find the problem soon.

Thanks for the help

Charles-Alexandre Mattelaer

Op 3 mei 2017 8:18 p.m. schreef "David Case" <>:

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

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
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
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

...good luck...dac

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Received on Wed May 03 2017 - 12:00:02 PDT
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