Dear Dan,
Thank you for your email. I appreciate it. I will look into amber 15
manual for cpptraj.
I read some old messages on ptraj and cpptraj last night. I also found
your tutorial on h bond analysis using cpptraj. I have two specific
questions based on what I have read:
(i) Is it true that ptraj cannot calculate intra-residue h bonds? Is
cpptraj able to calculate intra-residue h bonds.? I guess it is yes.
(ii) cutoff h bond angle of ptraj is 120 degree, cpptraj is 135 degree. Is
it true? Is it possible to change cut off angle if using cpptraj?
Best,
Wu
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Friday, April 15, 2016 10:36 AM
To: AMBER Mailing List
Subject: Re: [AMBER] hbond analysis of phosphotyrosine
Hi,
You could try using cpptraj, which you may find simpler as it can automate
selection of hydrogen bond donors/acceptors. Note that in cpptraj a
hydrogen bond donor is defined as the heavy atom bonded to the hydrogen,
which is opposite ptraj.
You could try e.g.:
hbond acceptormask :PTR out numhbond.dat avgout hbavg.dat
See the Amber 15 manual for more details.
-Dan
On Thu, Apr 14, 2016 at 8:55 PM, Wu Xu <wxx6941.louisiana.edu> wrote:
> Dear Amber users and developers,
>
> I want to analyze h bond which phosphotyrosine (nonstandard amino
> acid) phosphate oxygen is involved using ptraj. I included the
> following in the input file (attached)
>
>
> donor mask :PTR.OP1
>
> donor mask :PTR.OP2
>
> donor mask :PTR.OP3
>
>
>
> The output file (attached as well) gave me the following error
>
> PTRAJ: donor mask :PTR.OP1
>
>
> Mask [:PTR.OP1] represents 0 atoms !!!NO ATOMS DETECTED!!!
>
> WARNING in ptraj, donor: No atoms selected (:PTR.OP1), ignoring...
>
> PTRAJ: donor mask :PTR.OP2
>
> Mask [:PTR.OP2] represents 0 atoms !!!NO ATOMS DETECTED!!!
>
> WARNING in ptraj, donor: No atoms selected (:PTR.OP2), ignoring...
>
> PTRAJ: donor mask :PTR.OP3
>
> Mask [:PTR.OP3] represents 0 atoms !!!NO ATOMS DETECTED!!!
>
> WARNING in ptraj, donor: No atoms selected (:PTR.OP3), ignoring...
>
>
>
> Your suggestions will be much appreciated.
>
>
>
> Thanks,
>
>
>
> Wu Xu
>
>
>
> _______________________________________________
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> 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 307
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 Fri Apr 15 2016 - 10:30:03 PDT
