AMBER Archive (2005)

Subject: AMBER: Problem in ptraj

From: anshul_at_imtech.res.in
Date: Mon Jan 31 2005 - 16:23:30 CST


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
-------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu