Thanks, I'll check them out.
Regards
Tanmoy
On Mon, Jun 5, 2023 at 3:18 AM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Hi Tanmoy,
>
> it may not solve your problem, but the "ambmask" standalone command is
> very useful in debugging these kinds of things. You can experiment with
> what different mask strings would really correspond to in your system. As
> soon as my masks contain at least one &, @ or |, I usually test them with
> ambmask before using them in the real input file.
>
> Kind Regards,
>
> Thomas
>
>
>
> On Sun, Jun 4, 2023 at 7:51 AM Tanmoy Paul via AMBER <amber.ambermd.org>
> wrote:
>
>> Dear Amber Users,
>> I am trying to perform principal component
>> analysis in cpptraj. The input script is the following:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *parm 6ted_EC_dry.psftrajin combined_stride10.dcd 25001 last 5rms first
>> :1-7919&!.H=average crdset 6ted_pcacreatecrd 6ted_trajectoryruncrdaction
>> 6ted_trajectory rms ref 6ted_pca @N,CA,Ccrdaction 6ted_trajectory matrix
>> covar name 6ted_pca_covar .N,CA,Crunanalysis diagmatrix 6ted_pca_covar out
>> 6ted_eig_vec.dat vecs 5 name myEvecs nmwiz nmwizvecs 5 nmwizfile
>> 6ted_pca1.nmd nmwizmask @N,CA,Crunclear allreaddata 6ted_eig_vec.dat name
>> Evecsparm 6ted_EC_dry.psfparmstrip !(:1-7919.N,CA,C)parmwrite out
>> 6ted_modes.prmtoprunanalysis modes name Evecs trajout 6ted_mod1.nc
>> <http://6ted_mod1.nc> pcmin -100 pcmax 100 tmode 1 trajoutmask @N,CA,C
>> trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod2.nc
>> <http://6ted_mod2.nc> pcmin -100 pcmax 100 tmode 2 trajoutmask @N,CA,C
>> trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod3.nc
>> <http://6ted_mod3.nc> pcmin -100 pcmax 100 tmode 3 trajoutmask @N,CA,C
>> trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod4.nc
>> <http://6ted_mod4.nc> pcmin -100 pcmax 100 tmode 4 trajoutmask @N,CA,C
>> trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod5.nc
>> <http://6ted_mod5.nc> pcmin -100 pcmax 100 tmode 5 trajoutmask @N,CA,C
>> trajoutfmt netcdf*
>>
>> *But while running the script, I am getting the following error:*
>>
>> *Warning: No atoms in mask ':1-7919&@CA,N,C'*
>>
>> My system is relatively large. I tried running PCA without hydrogen, but
>> it
>> failed due to memory issues.(terminate called after throwing an instance
>> of
>> 'std::bad_alloc'
>> what(): std::bad_alloc
>> /var/spool/slurm/job1675329/slurm_script: line 9: 2989244 Aborted
>> (core dumped))
>>
>> Hence, I tried it with the backbone. I do not know what is wrong with the
>> musk. Any help will be greatly appreciated.
>>
>> Regards
>> Tanmoy
>>
>>
>>
>> --
>> With regards,
>> Tanmoy
>> _______________________________________________
>> 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,
Tanmoy
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Received on Mon Jun 05 2023 - 01:00:02 PDT
