Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 11 Aug 2017 13:03:44 -0400

Strange - maybe there was a formatting error in that email. While the
website is down you can find the latest version of the Amber manual in
$AMBERHOME/doc.

-Dan

On Fri, Aug 11, 2017 at 1:00 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> Dan,
>
> Thank you. That works.
>
> ambermd website and any tutorials are not loading today. I don't know why.
>
> I always look at manual first but today it is not loading either.
>
> So I found this in one from the email archives:
>
> Anyway, thank you for your quick response.
>
> From: Billy Miller III <brmilleriii.gmail.com
> <brmilleriii.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20Distance%20between%20two%20atoms%20vs%20time>
>>
> Date: Mon, 22 Mar 2010 08:57:13 -0400
>
> Once you trajin the correct trajectory file, the general command for
> calculating the distance between two atoms should be something like this:
>
> distance DIST .atom_number1 .atom_number2 out dist.out
>
> Or for your specific case, it should be:
>
> distance DIST .256 .399 out dist.out
>
> You could also use the residues numbers and atom types:
>
> distance DIST :154.OE1 :45.OD2
>
> Either of these last two commands should give you the exact same results
> for
> your system.
>
> Good luck!
>
> -Bill Miller
>
> On Fri, Aug 11, 2017 at 12:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> On Fri, Aug 11, 2017 at 12:42 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
>> >
>> > distance DIST1 .3981.3092 out dist1.out
>> >
>> > distance DIST :3981.O :3092.OH
>>
>> None of your mask expressions are valid. The symbol for atom is '.'.
>> You want something like:
>>
>> distance DIST1 .3981 @3092 out dist1.out
>>
>> The cpptraj section of the Amber manual has a good explanation of
>> Amber mask syntax (28.2.2 Atom Mask Selection Syntax, page 555). The
>> tutorials are also a good place to start:
>> http://ambermd.org/tutorials/#analysis
>>
>> Out of curiosity, what example were you using that recommended using a
>> period in the atom mask?
>>
>> -Dan
>>
>> >
>> > And I got no output with the following message :
>> >
>> > parm x.prmtop
>> > Reading 'x.prmtop' as Amber Topology
>> >> trajin Prod.mdcrd
>> > Reading 'Prod.mdcrd' as Amber NetCDF
>> >> distance DIST :3981.O :3092.OH
>> > DISTANCE: :3981.O to :3092.OH, center of mass.
>> >> run
>> > ---------- RUN BEGIN -------------------------------------------------
>> >
>> > PARAMETER FILES (1 total):
>> > 0: x.prmtop, 55934 atoms, 17450 res, box: Orthogonal, 17179 mol, 17171
>> > solvent
>> >
>> > INPUT TRAJECTORIES (1 total):
>> > 0: 'Prod.mdcrd' is a NetCDF AMBER trajectory, Parm x.prmtop (Orthogonal
>> > box) (reading 9000 of 9000)
>> > Coordinate processing will occur on 9000 frames.
>> >
>> > BEGIN TRAJECTORY PROCESSING:
>> > .....................................................
>> > ACTION SETUP FOR PARM 'x.prmtop' (1 actions):
>> > 0: [distance DIST :3981.O :3092.OH]
>> > :3981.O (0 atoms) to :3092.OH (0 atoms)
>> > Warning: One or both masks have no atoms.
>> > Warning: Setup incomplete for [distance]: Skipping
>> > ----- Prod.mdcrd (1-9000, 1) -----
>> > 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>> >
>> > Read 9000 frames and processed 9000 frames.
>> > TIME: Avg. throughput= 203.0209 frames / second.
>> >
>> > ACTION OUTPUT:
>> >
>> > DATASETS (1 total):
>> > DIST "DIST" (double, distance), size is 0
>> >
>> > RUN TIMING:
>> > TIME: Init : 0.0000 s ( 0.00%)
>> > TIME: Trajectory Process : 44.3304 s (100.00%)
>> > TIME: Action Post : 0.0000 s ( 0.00%)
>> > TIME: Analysis : 0.0000 s ( 0.00%)
>> > TIME: Data File Write : 0.0000 s ( 0.00%)
>> > TIME: Other : 0.0000 s ( 0.00%)
>> > TIME: Run Total 44.3305 s
>> > ---------- RUN END ---------------------------------------------------
>> >> quit
>> > ------------------------------------------------------------
>> --------------------
>> > To cite CPPTRAJ use:
>> > Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software
>> for
>> > Processing and Analysis of Molecular Dynamics Trajectory Data". J.
>> Chem.
>> >
>> >
>> >
>> > Any inputs would be greatly appreciated.
>> >
>> >
>> > Jag S
>> >
>> > Michigan State U
>> > Chemistry
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Aug 11 2017 - 10:30:03 PDT
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