Dear AMBER Users,
In the avg.dat file that are generated from "avout" (containing average
distances). I can not understand the values that ate written in the file.
Thanking You
On Wed, Dec 20, 2023 at 8:28 PM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Sorry, that I dont know, I havent used that.
>
> Since the documentation for this command is basically a single line in the
> manual, it may be better to check with the original author,
>
> Kind Regards,
>
> Thomas
>
> On Wed, Dec 20, 2023 at 3:28 PM Dulal Mondal <
> babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
>
>> Thank you, sir, for your reply. I am trying this using stfcdiffusion
>> command. Because I am trying to calculate the MSD of active site water
>> molecules (waters within 8 angstrom from Zn atom).
>> so parm *.prmtop
>> trajin *.nc
>> rms first #(as you recommended for internal coordinate changes)
>> stfcdiffusion mask :WAT.O out msd.dat time 5 mask2 :ZN6 lower 2.0 upper
>> 8.0 nwout nw.dat avout avg.dat
>> go
>> Can I do that for active site MSD of water molecules?
>> Thanking you
>>
>> On Wed, Dec 20, 2023 at 6:21 PM Steinbrecher, Thomas <
>> thomas.steinbrecher.roche.com> wrote:
>>
>>> Are you interested in diffusive motion of your molecules or in internal
>>> coordinate changes? For the later you need to align the trajectory to
>>> remove translational and rotational motion, for the former you should not
>>> align it.
>>>
>>> For wrapping, based on the manual, the diffusion command in cpptraj does
>>> handle imaging automatically (see the noimage keyword of that command as
>>> well), so it can process both wrapped and unwrapped trajectories. The only
>>> thing that seems to not work is wrapped trajectories plus the noimage
>>> keyword.
>>>
>>> In any case, why not try both options and see if the results make sense?
>>>
>>> Kind Regards,
>>>
>>> Thomas
>>>
>>> On Wed, Dec 20, 2023 at 11:30 AM Dulal Mondal via AMBER <
>>> amber.ambermd.org> wrote:
>>>
>>>> **Warning** The sender address (Dulal Mondal via AMBER ) can not be
>>>> verified, sender email address could be spoofed. Please take care to
>>>> proceed.
>>>> Dear Experts,
>>>> I am trying to calculate mean square displacement using cpptraj. In the
>>>> input file ("mdin"), I set the iwrap=1 command. Is it mandatory to
>>>> unwrap
>>>> the trajectory before analysis?
>>>> Again, is it mandatory to align the trajectory?
>>>>
>>>> Thanking You
>>>> --
>>>> *With regards,*
>>>> *Dulal Mondal,*
>>>> *Research Scholar,*
>>>> *Department of Chemistry,*
>>>> *IIT Kharagpur, Kharagpur 721302.*
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>
>>> --
>>> *Dr. Thomas Steinbrecher*
>>> Principal Scientist CADD
>>>
>>> Roche Pharma Research and Early Development
>>> Roche Innovation Center Basel
>>> F. Hoffmann-La Roche Ltd
>>> Bldg. 092/3.92
>>> Grenzacherstrasse 124
>>> 4070 Basel
>>> Switzerland
>>>
>>> Phone +41 61 682 1319
>>> mailto: thomas.steinbrecher.roche.com
>>>
>>
>>
>> --
>> *With regards,*
>> *Dulal Mondal,*
>> *Research Scholar,*
>> *Department of Chemistry,*
>> *IIT Kharagpur, Kharagpur 721302.*
>>
>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Dec 20 2023 - 08:30:02 PST
