[gmx-users] Seg Fault during pdb2gmx in demo

[Eric Edward Keaveny]

Hi,

To start, I'm using gromacs-3.1.4 with cygwin-1.3.22-1 and gcc-3.2-3.

I've been getting a seg-fault when trying to run the demo.

Here are the last 5 lines of the pdb2gmx "pop up window" output:

-posrefc	real  1000 Force constant for position restraints
-dummy   	enum  none Convert atoms to dummy atoms: none, hydrogens 
			   or aromatics
-[no]heavyh	bool  no   Make hydrogen atoms heavy
-[no]deuterate  bool  no   Change the mass of hydrogen to 2 amu

In the demo run window I get:

Press <enter>
Starting pdb2gmx
[1] 3452
Segmentation fault (core dumped)
pdb2gmx finished
Press <enter>

And finally, the contents of the pdb2gmx.exe.stackdump file:

Exception: STATUS_ACCESS_VIOLATION at eip=004572EA

eax=20312020 ebx=002263BC ecx=00000000 edx=002263BC esi=002263C2 
edi=00455688

ebp=100304F4 esp=00225390 
program=C:\cygwin\usr\local\gromacs\i686-pc-cygwin\bin\pdb2gmx.exe

cs=001B ds=0023 es=0023 fs=0038 gs=0000 ss=0023

Stack trace:

Frame     Function  Args

100304F4  004572EA  (00000000, 00030484, 100315F8, 00000400)

10031649  000003AF  (20322020, 20414320, 53594C20, 20202020)

      5 [main] pdb2gmx 616 handle_exceptions: Error while dumping state 
(probably corrupted stack)

Anyone have any ideas or suggestions as to how to fix this problem?

Eric