[AMBER] Problems with Antechamber leading to failed minimization

From: Charlotta Lebedenko via AMBER <amber.ambermd.org>
Date: Sun, 31 Jul 2022 16:16:15 -0400


I am trying to run a simulation of ionic liquids at room temperature.
My goals are similar to what is run in this tutorial:

However, when I try to run the first energy minimization of the system with
Sander, I immediately get this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory

Backtrace for this error:

#0 0x7fe9d1d7632a

#1 0x7fe9d1d75503

#2 0x7fe9d1790f0f

#3 0x5569ff4980e0

#4 0x5569ff3da4eb

#5 0x5569ff4317cb

#6 0x5569ff41e760

#7 0x5569ff417b32

#8 0x5569ff417b8e

#9 0x7fe9d1773c86

#10 0x5569ff26e9e9

#11 0xffffffffffffffff

[1]+ Segmentation fault (core dumped) sander -O -i minim.in -o
minim.out -p box_solv.prmtop -c box_solv.inpcrd -r minim.rst7 -x minim.nc
-e minim.dat

After reading about this error in past Amber emails, I tried using the
Check function in cpptraj, and this is the beginning of what it gives me:

This leads me to believe that the original molecule from Antechamber is
somehow wrong. I normally draw and minimize my molecules in Chemdraw and
then run that through antechamber, but for some reason these ionic liquid
molecules do not run through antechamber well. I have also tried drawing my
molecules in Pymol and Maestro, and I have tried using both pdb files and
mol2 files as input to antechamber, but I always get the same error when I
attempt energy minimization of the solvated system with Sander. I have
attached some input pdb and mol2 files as well as the output mol2 files I
get from antechamber (the ones with sqm in the name). It seems that
antechamber gets rid of my double bonds and charges. Please let me know if
you see anything obviously wrong with these files.

This is what I normally run in antechamber:

antechamber -i choline_pymol.mol2 -fi mol2 -o choline_pymol_sqm.mol2 -fo
mol2 -c bcc -s 2 -at gaff -nc +1

Thank you so much,
Charlotta Lebedenko

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Received on Thu Aug 04 2022 - 13:37:49 PDT
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