RE: AMBER: AMBER tutorial ambpdb question

From: Ross Walker <>
Date: Mon, 10 Jan 2005 18:14:49 -0800

Dear Kara,

You are not the first person to come across this problem. See:

I think I took a look at the ambpdb code sometime in November and fixed a
load stuff since the amber9 development version differs from the amber8
version and has several comments in there regarding fixing segmentation
faults. However, it seems I never fixed the amber8 version or released a bug
fix. I think because there are some major differences between the amber9
version and the amber8 version. The amber9 version supports dynamic memory
allocation for starters.

I have attempted to make a patch file for version 8 ambpdb.f that will add
dynamic memory allocation and "hopefully" fix the segmentation fault. I have
attached it to this email. You are welcome to try it out.

You will need to get a pristine version of amber8 and apply bugfix.all (or
at the very least bugfix.11) to the src tree (see amber website). Then apply
my bugfix with:

cp ambpdb_test_patch.txt $AMBERHOME/
patch -p0 <ambpdb_test_patch.txt

You should see:
"patching file src/etc/ambpdb.f" - Or something similar (I.e. no errors).

Then do
cd $AMBERHOME/src/etc
make ambpdb
cp ambpdb ../../exe/

Then see if the new ambpdb works. It works for me on an Intel P4 using ifort
8.1. Please let me know if it works for you. If it does I will post an
official bugfix.

Please note, this patch contains no warranty whatsoever...

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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> -----Original Message-----
> From:
> [] On Behalf Of Kara Wald
> Sent: 10 January 2005 17:34
> To:
> Subject: AMBER: AMBER tutorial ambpdb question
> I'm a relatively new user of Amber and have been going
> through the DNA
> tutorial. I can't get ambpdb to work. I type in: ambpdb -p
> polyAT_vac.prmtop < polyAT_vac_init_min.rst >
> polyAT_vac_init_min.pdb
> and get the message: Segmentation fault.
> I tried looking up ambpdb in the Amber 8 manual, but it didn't help.
> Thanks,
> Kara Di Giorgio
> I'm running on a G4 Powerbook.
> --------------------------------------------------------------
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Received on Tue Jan 11 2005 - 02:53:00 PST
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