Dear All,
While trying this structure for heat jobs I get the following error in one
of the output files and it seems that job stops writing in heat.out without
additional messages.
Can you please suggest how to fix this? should I try suggestions given here
<
http://archive.ambermd.org/200703/0381.html>, here
<
http://archive.ambermd.org/201402/0332.html>or better options are
available in Amber19?
I am trying by removing the restraints during min job, but it's in the
queue at the moment.
thank you very much for your suggestions.
[xxxxx.hlogin1 rup-3a4-implicit]$ more amber-heat.o494747
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 2874 5712 5714
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
On Thu, Jun 27, 2019 at 2:42 PM David Case <david.case.rutgers.edu> wrote:
> On Thu, Jun 27, 2019, Vaibhav Dixit wrote:
>
> >I tried the cpptraj checkstructure command, but it doesn't print anything
> >in the reportfile.generated file (min-structure.txt, the file is empty).
>
> This means that cpptraj found no bad contacts or unusally long bonds,
> within
> the tolerances that cpptraj uses. I think maybe(?) cpptraj has a cutoff of
> 0.8 Ang, whereas leap has a larger cutoff.
>
> ....dac
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
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Received on Thu Jun 27 2019 - 08:00:03 PDT
