Sent from my iPad
> On Sep 21, 2017, at 11:53 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> On Thu, Sep 21, 2017 at 11:36 AM, Mo Rahman
> <mo.rahman.postgrad.manchester.ac.uk> wrote:
>> First, I believe I need to obtain an average structure, stripped of solvent, and for that I used the the following input:
>>
>> parm ~/entropy-md/alanine/setup/ala-solv.prmtop #(topology file of the alanine dipeptide in solution)
>> trajin ~/entropy-md/alanine/production/ala-solv-prod.mdcrd
>> autoimage
>> strip :WAT
>> average ala-avg.mdcrd crd nobox
>
> Typically you obtain an averaged structure for QH calculations in
> order to RMS best-fit trajectory coordinates to it in order to remove
> overall rotational/translational motion. If this is indeed what you
> want, you also need to have an 'rms' command prior to your 'average'
> command, otherwise your average structure will contain contributions
> from these motions which is probably not what you want.
>
>> This completes successfully, however the next step, the actual QH calculation fails to complete. I used the following script:
>>
>> parm ~/entropy-md/alanine/setup/ala-vac.prmtop #(topology file of the alanine dipeptide alone)
>> trajin ala-avg.mdcrd
>> createcrd ala-avg.nc
>> crdaction ala-avg.nc mwcovar name arcov out arcov.dat
>> runanalysis diagmatrix arcov out qh.out thermo outthermo thermo.dat temp 300
>
> This input is definitely not what you want. You're reading your
> average coordinates as the input trajectory, then queuing up an action
> that creates a coordinates (COORDS) data set from that input
> (createcrd), and then trying to use that COORDS data set before its
> even created. I recommend reading the manual so that you understand
> what each of these commands do and become familiar with how Actions
> and Analyses work in cpptraj.
>
> First, you want to generate your covariance matrix from your input
> trajectory (ala-solv-prod.mdcrd), not the average structure. You may
> want to rms-fit to the average structure as I previously mentioned, in
> which case you need to load it as a reference:
>
> parm ~/entropy-md/alanine/setup/ala-solv.prmtop #(topology file of the
> alanine dipeptide in solution)
> trajin ~/entropy-md/alanine/production/ala-solv-prod.mdcrd
> reference ala-avg.mdcrd
> strip :WAT
> rms reference
>
> You then want to create the covariance matrix; this is done via the
> 'matrix' command (which you didn't actually include before, just its
> keywords).
>
> matrix mwcovar name arcov out arcov.dat
>
> You can save the rms-fit coordinates via 'createcrd' if you want to
> later use them for projection in this run, but otherwise it's not
> necessary. You then want to use the 'diagmatrix' command, but there is
> an important distinction to be made. The 'runanalysis <cmd>' command
> means to run the analysis *now*, whereas specifying the analysis
> command by itself will queue it up after any actions, which is what
> you want in this case.
>
> diagmatrix arcov out qh.out thermo outthermo thermo.dat temp 300
>
> In order to use the 'runanalysis' command successfully you would need
> to execute the trajectory processing run first so that the matrix is
> created:
>
> run
> runanalysis diagmatrix ...
>
> Hope this helps.
>
> -Dan
>
> PS - You may find some of these cpptraj tutorials useful:
> http://ambermd.org/tutorials/#analysis
>
>>
>> The second script seems to fail after createcrd is invoked, and cpptraj reports that the trajectory file contains no frames: the same thing happens when I load in a trajectory with just the solvent removed, but not averaged.
>>
>> Any help with this would be greatly appreciated.
>>
>> As an additional request, I would be grateful for any assistance/pointers to guidance for performing normal mode analysis of my output, to obtain entropy using that method as well.
>>
>> Kind regards,
>>
>> Mo
>> _______________________________________________
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>> 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
>
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Received on Thu Sep 21 2017 - 20:30:03 PDT
