AMBER Archive (2004)

Subject: AMBER: file corruption with ptraj

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Mon Oct 18 2004 - 10:10:51 CDT

Hello Amber group

Thanks for the responses. I really appreciate the help.

Last Friday I wrote about a problem with combined trajectory files. When
I combined these mdcrd files (file1 and file2) together and attempted to
obtain RMSd, I got a message that the combined trajectory files were
corrupted at frame 340.

Here is some more information that was asked for:

>where is frame 340 in the original trajectories, file1 or file2?

The 340 frame is in file1.mdcrd and it is not at the end the frame.
File1.mdcrd has 999 frames.

>did you view the combined file using a graphical program like vmd or
moil-view?

Not until you suggested it. Now I have used moil-veiw on the combined
file called file1_2.mdcrd. Atoms appeared to be moving by 10 or more
angstroms within 5 ps frames making bonds just as long. Obviously,
Something has gone wrong with the trajectory files.

What I discovered through many attempts is that whenever I remove (strip
water) using ptraj it corrupts the output trajectory files. For example,
below I show the script were I removed the water trajectories:

trajin file1.mdcrd

trajin file2.mdcrd

strip :WAT

tarjout file1_2.mdcrd

box x 51.1333056 y 50.7934380 z 72.1834321

center :1-198 origin

image :199-398 origin center familiar

go

I should state that the output of this above process shows a successful
job. I then attempted to obtain RMSd from file1_2.mdcrd using ptraj
(script shown below).

trajin file1_2.mdcrd

box x 51.1333056 y 50.7934380 z 72.1834321

center :1-198 origin

image :199-398 origin center familiar

rms first mass out trial1_2all_backboneflux.txt time 5 @CA,C,N

atomicfluc out trial1_2residueflux.txt :1-398 byres

go

The output file once again, gave a message saying there was a corruption
found in the trajectory file at step #340 :

Processing AMBER trajectory file file1_2.mdcrd

Set 1 .................................................

Set 50 .................................................

Set 100 .................................................

Set 150 .................................................

Set 200 .................................................

Set 250 .................................................

Set #340 appears corrupted (

51.133 50.793 72.183)

Set 300 .......................................

PTRAJ: Successfully read in 339 sets and processed 339 sets.

Dumping accumulated results (if any)

PTRAJ RMS: dumping RMSd vs time data

PTRAJ ATOMICFLUCT: Dumping atomic positional fluctuations

logout

Now, if I LEAVE OUT the "strip :WAT" command in the above input file
there is no corruption found in the output trajectories and I have no
problem obtaining the RMSds.

Thus, it appears that stripping the water is causing the problem in my
case. I have no idea why this is occurring. Am I doing something clearly
wrong? I have attached my MD input file just so you see everything I am
doing from the beginning.

Thanks again for you assistance.

Steve


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