PS - You may also want to try the new 'nativecontacts' command in
cpptraj - it is faster than the 'contacts' command, has a few more
features, and may be a bit more robust. The command would be (based on
the input you sent me):
nativecontacts first byresidue .CA distance 6.0 out testing_md1.out
See the Amber 14 manual for further options (such as writing out a
contacts map).
-Dan
On Mon, Apr 28, 2014 at 1:22 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I was able to run cpptraj successfully on the
> input/topology/trajectory you provided (see attached output). Did you
> get a segfault using the same input/topology/trajectory? If you did,
> then have you run all tests on your Amber installation and did they
> pass?
>
> Otherwise, re-run your calculation with 'debug 5' as your first
> command and send me (off-list) the complete output from cpptraj
> (STDOUT and STDERR).
>
> -Dan
>
>
> On Sat, Apr 26, 2014 at 10:44 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> 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)
>
>
>
> --
> -------------------------
> 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)
--
-------------------------
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)
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Received on Mon Apr 28 2014 - 13:00:02 PDT
