Re: [AMBER] Ptraj crashes and Hbond analysis

From: Daniel Roe <>
Date: Wed, 23 Mar 2011 09:45:14 -0400


In order to help diagnose the problem we need to try and reproduce it.
To that end please provide:

1) Version of ptraj used (e.g. AmberTools 1.4) and bugfixes applied (if any)
2) Which compilers were used to build ptraj and what version
3) The exact ptraj input that causes the error
4) The output that ptraj produces
5) If possible, attach the topology and restart (or 1 frame of
trajectory) files of the system you are using. If this is not possible
for whatever reason, please provide system details, i.e. number of
atoms, number of frames in traj, whether the system is periodic etc.

Providing all of the above information will make it easier for us to
understand any bugs that may be occurring and ultimately easier to
help you.



On Wed, Mar 23, 2011 at 9:01 AM, Kamali Sripathi <> wrote:
> Dear Dr. Cheatham,
> Thank you very much for your response.
> On Tue, Mar 22, 2011 at 7:33 PM, Thomas Cheatham III <> wrote:
>> There is insufficient information provided to comment.
> This is very true; sorry for not being more specific. The ptraj script that
> I'm referring to has about 18 distance commands, one angle command, and
> three dihedral commands. My system is an RNA system of 85 nucleotides, and
> I've been running simulations on the wild-type structure as well as 8
> structures with 1 base pair mutated. I slightly modify some distance
> commands in my ptraj script to apply it to each of the 9 structures. I'm
> frustrated because it works for, say, mutants 2-8, but I consistently get
> seg faults when I use it for the wild-type and mutant 1 structures.
> Please let me know if you need more information.
> Thanks again, and have a great day,
> Kamali
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Mar 23 2011 - 07:00:04 PDT
Custom Search