Hi,
On Fri, Apr 15, 2016 at 11:09 AM, Wu Xu <wxx6941.louisiana.edu> wrote:
> 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.
Both ptraj and cpptraj are able to calculate intra-residue hydrogen
bonds. It just depends on what donors and acceptors you define.
Cpptraj has a few more features that ptraj in that it can do imaged
hbonds, only inter-molecular hbonds, etc.
> (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?
Yes, use the 'angle' keyword. Specifying an angle of -1.0 disables the
angle cutoff. See the Amber 15 manual for more details.
-Dan
>
> 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
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> 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 Sat Apr 16 2016 - 10:00:03 PDT
