AMBER Archive (2009)

Subject: [AMBER] Seg-fault when creating residue

From: Valla Fatemi (
Date: Tue Jun 16 2009 - 20:28:43 CDT

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

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?


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