Dear Dan,
Thank you for your suggestions. It seems worked. I need to read the tutorial to understand H-bond analysis better.
The analyse_hbond_1.out for the first traj is attached.
Best regards,
Wu
----- Original Message -----
From: "Daniel Roe" <daniel.r.roe.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Monday, May 30, 2011 8:19:43 AM
Subject: Re: [AMBER] H-bond analysis
Hi,
I see several issues with your output. First, it appears that you're
using MPI to run 8 single-threaded copies of ptraj at a time, which
can cause big problems with output since all the copies will attempt
to write to the same files. Don't use mpirun or mpiexec to run serial
ptraj, it's not necessary. It also really confuses the output and
makes it difficult to locate errors.
Second, you have several messages like this:
...
PTRAJ: acceptor mask :HIP.ND1,NE2 :HIP.HE2,HD1
Mask [:HIP.ND1,NE2] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:HIP.HE2,HD1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :2-11,13-16,20.N and :2-20.H which
contain 15 and 19
atoms respectively. Ignoring...
...
And ultimately:
...
NO ACTIONS WERE SPECIFIED
...
This means the hbond command wasn't successfully set up, but since
your output is jumbled from the extra threads it's tough to tell
exactly what happened. Run a short test first (1 thread only!) reading
in only 10 frames of your trajectory or so (i.e. use "trajin
equil_1-10.binpos 1 10") and check that output for problems. Also,
double check your mask expressions; note that for reasons of backwards
compatibility the definitions of hydrogen bond "donor" and "acceptor"
are reversed in ptraj w.r.t. the standard convention.
Let me know if you still have problems.
-Dan
On Mon, May 30, 2011 at 8:01 AM, Wu Xu <wxx6941.louisiana.edu> wrote:
> Dear Amber developers and users,
>
> I am doing MD simulations for human CycC almost exactly following the steps in the tutorial 3 (section 1-6) using Amber 11. I conducted H bond analysis and obtained analyse_hbond.out (http://ambermd.org/tutorials/basic/tutorial3/section6.htm).
>
> No H-bonds were detected by this analysis, but I am not sure about this result.
>
> The analyse_hbond.out is attached.
>
> My question is: can I say no H-bonds or some errors due to my lack of experience in MD simulation?
>
> Thanks for your time!
>
> Wu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon May 30 2011 - 15:30:02 PDT
