Re: [AMBER] segmentation fault on tleap

From: Giorgos Lamprinidis <>
Date: Wed, 6 Jul 2011 10:58:48 +0300

I thank you all for your replies....
Finally I tried my last...hope ...i downloaded intel c++ and fortran
compiler(evaluation version), I compiled both ambertools 1.2 and ambertools
1.5 and now I don't get seg fault when I load leaprc.ff99SB on both version.
I hope everything else will run without problems.


-----Original Message-----
From: David A Case []
Sent: Tuesday, July 05, 2011 7:03 PM
To: AMBER Mailing List
Subject: Re: [AMBER] segmentation fault on tleap

On Tue, Jul 05, 2011, Giorgos Lamprinidis wrote:

> Now i have a new computer running Fedora core 15 (64bit).

Fedora 15 was released on 24 May 2011, after the release of AmberTools 1.5.
As you can see from searching the mailing list archives, there are a number
of problems related to Amber, especially (only?) for the 64-bit version.
We are trying to get Amber developers to set up virtual machines with this
in order to get at the problems, which (plausibly) are related to the very
recent version of gcc that is being used.

I think the seg fault you report with AT1.2 is indeed fixed in more recent
versions, but the latter don't seem to compile with Fedora 15. Others can
post their experience here, but I don't have any simple workaround.

You indicate that you still have a older pc, so I hope you can use
there, then copy the files to the new machine for running sander or pmemd.
One thing to try is to see if downgrading the compiler will help: use gcc4.5
instead of gcc4.6.


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