AMBER Archive (2007)

Subject: AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap

From: Laura McDriscoll (laura_ann_mcdriscoll_at_hotmail.com)
Date: Thu Mar 15 2007 - 23:59:33 CST

I am trying to do a simulation of NaCl in H2O solution using periodic
boundary conditions and AMBER 6 package. I am using xleap to set up my
system with the unit editor. Briefly, I imported one Na+ unit, one Cl-
unit, then closed the editor. I then used the solvateBox command to solvate
my system:

solvateBox system WAT 20 iso

The solvated system looks fine in the unit editor, but when I try to save my
prmtop and inpcrd files using:

saveAmberParm system system.top system.crd

I get a segmentation fault (core dumped) message and xleap exits
automatically.

Does anyone know what I did wrong? I only have problems saving inpcrd and
prmtop files when a periodic boundary condition is imposed. All other
systems save with no problem.

Thanks

Laura McDriscoll

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