Dear Dr. Case,
Thank you very much for the email. We use ambertools 1.4 version.
This is the information about the OS/compiler on our cluster in the
following. We have more than 207 atoms in the system. We just read over an
email in the mailing list that suggested us to use AMBER11 for
parameterization of large organic molecules like ours. Could you recommend
it too? I can ask my advisor to purchase it.
Thank you very much.
Sincerely,
Guoxiong
"It is AmberTools 1.4 and there was a bugfix applied. When it was compiled
I used
configure intel
and the intel compiler version is 10.1.
[jsarlo.cusco ~]$ uname -a
Linux cusco 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST 2010 x86_64
x86_64 x86_64 GNU/Linux
[jsarlo.cusco ~]$ gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
The antechamber test cases passed when it was installed and I just ran them
again to make sure and they passed again.
If you need anything else, let us know."
On Thu, Aug 5, 2010 at 2:48 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Aug 05, 2010, Guoxiong Su wrote:
> >
> > I am trying to use antechamber to create parameter and coordinate files
> for
> > my molecule. Then I run "antechamber -i input.pdb -fi pdb -o output.mol2
> -fo
> > mol2 -c bcc -s 2". The job was aborted after running 130 hours and I got
> the
> > error message as follow:
> >
> > Total number of electrons: 910; net charge: 0
> >
> > Running: /share/apps/amber11/bin/sqm -O -i sqm.in -o sqm.out
> > *** glibc detected *** antechamber: free(): invalid next size (normal):
> > 0x000000000da83060 ***
> > ======= Backtrace: =========
> > /lib64/libc.so.6[0x3e89a722ef]
>
> We will need to see your "input.pdb" file, plus learn the following info:
>
> Which version of AmberTools?
> What OS, compiler version (type "uname -a" and "gcc --version" or
> equivalent)
>
> All we can do is try to reproduce it. I am assuming that all the
> antechamber
> test cases passed -- if not, let us know!
>
> ....dac
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 09 2010 - 09:00:05 PDT
