Hi Abhishek,
The error is loud and clear, the total number of atoms in the prmtop and the trajectory file are not matching, hence cpptraj cannot process it. This has nothing to do with the format of the trajectory file; *.crd should work as good as *.crd.gz, as Adrian suggested.
Check if you are loading the correct prmtop for the corresponding trajectory file.
Best Regards
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________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: 09 June 2017 00:03:58
To: AMBER Mailing List
Subject: Re: [AMBER] PCA analysis
Hi Dr.Adrian,
I have tried that but it is giving some error
Error: # atoms in current topology (57908) != # atoms in coords set "cpu-gpu-trajectories" (0)
Error: Setup failed for [createcrd]
Error: trajectory contains no frame
It seems it is reading crd.gz file as it can be seen in pca.out file that it has been processed.
I have also attached by pca.trajin file, if you can help in getting over this error.
Thanking you,
-AT
________________________________
From: Adrian Roitberg <roitberg.ufl.edu>
Sent: Thursday, June 8, 2017 5:55:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] PCA analysis
Did you try to see if it works ?
It should, but you should be using netcdf format fro all your jobs (.nc)
always. They occupy much less space, and the data input/output is MUCH
faster.
adrian
On 6/8/17 12:52 PM, Thakur, Abhishek wrote:
> Hi
>
> While seeing the script for PCA analysis I have found that it is asking for trajectory file in Y.nc format
>
> trajin cpu/cpu.nc parm [cpu]
>
> Can I use Y.crd.gz file? Which I have obtained by combining all 300ns of trajectory file after auto imaging it?
>
>
>
> Thanking you,
>
> -AT
>
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Received on Thu Jun 08 2017 - 22:00:03 PDT
