AMBER Archive (2009)

Subject: [AMBER] Re: Seg-fault when creating residue

From: Valla Fatemi (
Date: Wed Jun 17 2009 - 12:41:47 CDT

Addendum: I am using Amber10 with AmberTools 1.0

Please let me know if I left out any relevant information.


----- Original Message -----
From: Valla Fatemi <>
Date: Tuesday, June 16, 2009 6:28 pm
Subject: Seg-fault when creating residue

> I use a pdb file of molecule (created in molden) to create a .mol2
> and .frcmod files of it for later use as a solvent in normal MD
> runs. I follow EXACTLY the instructions indicated in tutorial B4.
> My frcmod file is empty, and everything runs just fine, until I
> open up xleap and attempt to load it as a unit (again, just as in
> tutorial B4). When I attempt this (with several molecules), I
> receive "Segmentation fault" in the linux terminal and xleap closes
> automatically.
> I noticed that pdb files created by molden are not formatted
> exactly teh same way as that in the tutorial, but it seams like the
> divcon.pdb file generated in the first step is more nearly the
> correct format. The differences are that lines in the file looks
> like this:
> ATOM C 2 0.000 0.000 0.000
> ATOM C1 2 1.422 0.000 0.000
> ...etc...
> I realize that each line (as well as the header) should include
> some some kind of a name that is a couple of characters long, but I
> successfully added that to the generated .mol2 files to get rid of
> those errors. Once or twice the unit loaded just fine, but those
> times when I subsequently did "list" in xleap to check on it, xleap
> would crash immediately with no error reported at all.
> The same segmentation faults occur when on such simple molecules as
> water.
> any thoughts as to what is going on here?
> -V

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