Dear Amber users,
I have done MD simulations ona protein using GB model. Since my process
war restarted a few times so I used Ptraj to combine the mdcrd files and
made a new one. then I used this file to get an average structure but got
this error:
------------------------------------------------------
Processing AMBER trajectory file bsa-grp3.mdcrd
Set 1 .................................................
Set 50 ........................................
ERROR in readAmberTrajectory(): fsetpos() failed on when looking for box
coordinates!
-----------------------------------------------------
In all there are 179 frames and I have not used any periodic box
conditions. If I run the same script of ptraj for indovidual mdcrd files,
I get the average structure. the new combined mdcrd file works well for
other kinds of analysis.
The ptraj script for getting the average structure is:
ptraj mod9.prmtop << EOF
trajin grp3.mdcrd
average grp3-avg-pr.pdb PDB
EOF
and the one to combine the mdcrd files is:
ptraj mod9.prmtop << EOF
trajin gbmd-pr.mdcrd
trajin gbmd-pr-1.mdcrd
trajin gbmd-pr-2.mdcrd
trajin gbmd-pr-3.mdcrd
trajin gbmd-pr-4.mdcrd
trajin gbmd-pr5.mdcrd
trajout grp3.mdcrd
EOF
Can anyone tell me where I am going wrong and how to rectify the problem.
with Thanks and best regards,
Anshul
-------------------------------------------------
Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352
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Received on Mon Jan 31 2005 - 12:53:01 PST
