Hi,
Does your Amber installation pass all tests? I am unable to reproduce
this segmentation fault with a similar system. Can you send me
(off-list) a small example that causes a segfault (topology and small
trajectory) so I can try and reproduce the error? Thanks.
-Dan
On Thu, Apr 24, 2014 at 5:48 PM, kara tuong vi ngo
<karatuongvi44.yahoo.com> wrote:
> Dear AMBER users,
>
> I just updated mine to amber 14, but I am still receiving the same problem "segmentation fault" when I run the native contact for my molecule (20 residues). I don't know what I did wrong.
>
> Thank you again!
>
>
> On Tuesday, April 22, 2014 8:20 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> Which version of cpptraj are you running (cpptraj --version)? If you
> are not using version 14.00 I recommend you upgrade to AmberTools 14
> (http://ambermd.org/AmberTools14-get.html).
>
> -Dan
>
>
>
> On Mon, Apr 21, 2014 at 11:59 PM, kara tuong vi <karatuongvi44.yahoo.com> wrote:
>> Dear Amber Users,
>>
>> I am trying to find the native contact for my molecule, but I keep getting "segmentation fault". I decided to use a smaller molecule with about 20 residues: TC5b_linear.pdb
>> The command I had was: cpptraj -p polyAT_wat.prmtop < testing_contact.in
>> The script for "testing_contact.in":
>> trajin polyAT_wat_md1.mdcrd
>> contacts first byresidue out testing_md1.out distance 6.0 .CA
>>
>> Thank you in advance!
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 26 2014 - 10:00:03 PDT
