Water ions removing step getting error -reg

[venkat]

Dear Sir, 

                Am new to this software, am trying to do CPCA  (my system prepared using CHARMM-GUI and simulations performed using NAMD) before proceeding to the Cartesian pca try to remove the water ions, I used following command 

carma64 -v -w -fit -atmid ALLID -segid A ../../step5_assembly.xplor_ext.psf ../test.dcd

but error get as following 

PSF with the EXT extension detected.

Less than two "     " atoms found for segid " A   ". Abort.

kindly let me know wrong i did ? and how perform correctly 

Thank you 

[Nicholas M. Glykos]

> Am new to this software, am trying to do CPCA (my system
> prepared using CHARMM-GUI and simulations performed using NAMD) before
> proceeding to the Cartesian pca try to remove the water ions, I used
> following command
>

> *carma64 -v -w -fit -atmid ALLID -segid A
> ../../step5_assembly.xplor_ext.psf ../test.dcd*

>
> but error get as following
>
> PSF with the EXT extension detected.
> Less than two " " atoms found for segid " A ". Abort.

Post the output from

head -100 step5_assembly.xplor_ext.psf





--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/

[venkat]

Dear Sir, 

              kindly check file  in that attachment

thank you  

[Nicholas M. Glykos]

> 1 PROA 4 ASP N NH3 -0.300000 14.0070 0 0.00000 -0.301140E-02
> 2 PROA 4 ASP HT1 HC 0.330000 1.00800 0 0.00000 -0.301140E-02

The SEGID of your protein is "PROA" and not "A" (as you told carma with the
"-segid A" flag.

[venkat]

Thank you sir now only noticed in psf file for selections 

carma64 -v -w -fit -atmid ALLID -segid PROA -segid PROB ../step5_assembly.xplor_ext.psf test.dcd

Thank you very much 

[Diana A. Valencia]

I would like to comment that in my cause the protein was segment 'U' (I don't know why) in .psf file. 

So I used the same command with '-segid U' and worked very well. 

Then remember always check the .psf file.