Thank you for sharing this Matias. It looks like space at the end got
included by accident. I checked the git version and though it finishes, it
slows down leap a lot.
I will get this fixed and it should be out in the next amber20 patch.
On Wed, May 20, 2020 at 1:14 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear developers,
>
> I've just found a format issue in the recently incorporated libraries for
> modified amino acids "mod_amino.lib" and "mod_amino19.lib".
>
> A blank space before the carrier returns at line 773 is causing LEAP to
> hang while sourcing cmd files "leaprc.protein.ff14SB_modAA" or
> "leaprc.protein.ff19SB_modAA" (see related thread: [
> http://archive.ambermd.org/201910/0094.html])...
>
> You can find the issue by executing the following command:
> grep -nE "\ $" mod_amino*.lib | cat -A
>
> mod_amino19.lib:773: "CA" "XC" 0 1 131072 3 6 -0.042993 $
> mod_amino.lib:773: "CA" "CX" 0 1 131072 3 6 -0.042993 $
>
> Best,
>
> Matias Machado
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
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>
--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Wed May 20 2020 - 14:30:01 PDT
