Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue

From: David Case <>
Date: Wed, 22 Feb 2017 14:27:21 -0500

On Wed, Feb 22, 2017, Nikolay N. Kuzmich wrote:
> here's the prepin file:

(Easier for us if you attach such files, since files often get mangled by mail

> the main chain file:

Not sure what you be using the above for(?)

> >
> > parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \
> > $AMBERHOME/dat/leap/parm/parm10.dat
> >
> > And then I got message "Segmentation fault".

Doesn't give a segfault for me, although it does complain about the DU atoms,
which is a bit strange. But parmchk2 is primarily designed for the gaff
force fields, so there might be something related to that. Which version
of AmberTools are you using?

I'm not following exactly your workflow here. The mol2 file has a carbon
with only three single bonds to it (C21); not sure if that has anything to do
with what you see or not. Also, I don't see anything obviously wrong with the
prepin file, and I can't reproduce the seg fault. Bottom line is that I'm
not able to provide much help here (unless it's just a matter of needing to
update to the current version of the codes.)

Can you say more about exactly what you did to create the prepin file?


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Received on Wed Feb 22 2017 - 11:30:03 PST
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