Re: [AMBER] Ptraj crashes and Hbond analysis

From: Kamali Sripathi <ksripath.umich.edu>
Date: Thu, 24 Mar 2011 09:36:28 -0400

Hi Dan,

1) The version of ptraj used is the one that comes with AMBER 10.
2) AMBER bugfixes 1-8 and AmberTools bugfixes 1-3 were applied (I'm using
AMBER and AmberTools on a cluster, and I wasn't the one that installed and
compiled them).
3) distances.ptraj and dihedrals.ptraj are the two ptraj scripts that I'm
having trouble with. Initially, they used to be one script. They're broken
into two because I thought that maybe putting all these commands into one
script caused the seg fault, but the scripts still aren't working.
4) distances.out and dihedrals.out are the two outputs from ptraj. ptraj
seems to crash right after the "checking coordinates" step or the
"processing coordinates" step.
5) I've been applying these ptraj scripts to a number of systems: a
wild-type 85-nt RNA system charge-neutralized with either Na+ or a
combination of Na+/Mg2+ and then mutants on this wild type structure, in
which one base pair is mutated from the wild-type. The mutant base pairs are
charge-neutralized with Na+, and the ptraj scripts have worked for them.
 It's only when I apply the scripts to the wild-type systems that ptraj
crashes. These mutants systems have between 60,000 and 70,000 atoms with
ions and waters added. The wild type systems have between 58,000 and 60,000
atoms. All systems are periodic, use explicit TIP3P water, and each traj
file has 100 ps in it (= 100 frames). Please let me know if you need me to
provide any other information.

Thank you so much, and have a great day,

Kamali Sripathi

On Wed, Mar 23, 2011 at 2:44 PM, Kamali Sripathi <ksripath.umich.edu> wrote:

> Hi Dan,
>
> Thank you for your response. I'm just waiting on the bugfixes that were
> used, and then I'll be able to send you a reply to your questions.
>
> Thanks again, and have a great day,
>
> Kamali Sripathi
>
>
> On Wed, Mar 23, 2011 at 9:45 AM, Daniel Roe <daniel.r.roe.gmail.com>wrote:
>
>> Hi,
>>
>> 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.
>>
>> Thanks!
>>
>> -Dan
>>
>> On Wed, Mar 23, 2011 at 9:01 AM, Kamali Sripathi <ksripath.umich.edu>
>> wrote:
>> > Dear Dr. Cheatham,
>> >
>> > Thank you very much for your response.
>> >
>> > On Tue, Mar 22, 2011 at 7:33 PM, Thomas Cheatham III <tec3.utah.edu>
>> 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.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>


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Received on Thu Mar 24 2011 - 07:00:03 PDT
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