Hello Amber developers and users,
I am having problems with ptraj analysis of a trajectory and would appreciate any guidance.
Following the simulation of a system for 15ns (trajectory file of 75 000 frames), I am attempting to analyze the trajectory with an RMSD calculation with ptraj. After reading in the trajectory files and striping the solvent and ions, I use the commands "center .CA mass origin" and "image origin center, and then calculate the mass weighted RMSD with respect to the first frame in 3 ways: (1) of C-alpha atoms, (2) of the protein backbone, (3) of all atoms.
I get 2 errors when doing this.
Error 1 in the .out file. About 75% to 100% though processing the Amber trajectory, I get the error:
Too many iterations in routine JACOBI
convergence failed
Error 2:
*** glibc detected *** /home/mariusz/LOCAL/amber/amber12/bin/ptraj: free(): invalid pointer: 0x00000000016555a0 *
======= Backtrace: =========
/lib64/libc.so.6[0x3b7b275296]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x421ae2]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x48e9af]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x4491e3]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x45231c]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x437aa8]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x4028e7]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3b7b21ecdd]
/home/mariusz/LOCAL/amber/amber12/bin/ptraj[0x4023b9]
======= Memory map: ========
00400000-0055f000 r-xp 00000000 08:12 10495397 /home/mariusz/LOCAL/amber/amber12/bin/ptraj
0075e000-00768000 rw-p 0015e000 08:12 10495397 /home/mariusz/LOCAL/amber/amber12/bin/ptraj
00768000-0076c000 rw-p 00000000 00:00 0
00953000-07893000 rw-p 00000000 00:00 0 [heap]
3b7ae00000-3b7ae20000 r-xp 00000000 08:02 8126466 /lib64/ld-2.12.so
3b7b01f000-3b7b020000 r--p 0001f000 08:02 8126466 /lib64/ld-2.12.so
3b7b020000-3b7b021000 rw-p 00020000 08:02 8126466 /lib64/ld-2.12.so
3b7b021000-3b7b022000 rw-p 00000000 00:00 0
3b7b200000-3b7b386000 r-xp 00000000 08:02 8126470 /lib64/libc-2.12.so
3b7b386000-3b7b586000 ---p 00186000 08:02 8126470 /lib64/libc-2.12.so
3b7b586000-3b7b58a000 r--p 00186000 08:02 8126470 /lib64/libc-2.12.so
3b7b58a000-3b7b58b000 rw-p 0018a000 08:02 8126470 /lib64/libc-2.12.so
3b7b58b000-3b7b590000 rw-p 00000000 00:00 0
3b7be00000-3b7be83000 r-xp 00000000 08:02 8126486 /lib64/libm-2.12.so
3b7be83000-3b7c082000 ---p 00083000 08:02 8126486 /lib64/libm-2.12.so
3b7c082000-3b7c083000 r--p 00082000 08:02 8126486 /lib64/libm-2.12.so
3b7c083000-3b7c084000 rw-p 00083000 08:02 8126486 /lib64/libm-2.12.so
3b88600000-3b88616000 r-xp 00000000 08:02 8126525 /lib64/libgcc_s-4.4.6-20110824.so.1
3b88616000-3b88815000 ---p 00016000 08:02 8126525 /lib64/libgcc_s-4.4.6-20110824.so.1
3b88815000-3b88816000 rw-p 00015000 08:02 8126525 /lib64/libgcc_s-4.4.6-20110824.so.1
7f813c9c9000-7f81403b0000 rw-p 00000000 00:00 0
7f81403b0000-7f81404a0000 r-xp 00000000 08:02 4195479 /usr/lib64/libgfortran.so.3.0.0
7f81404a0000-7f814069f000 ---p 000f0000 08:02 4195479 /usr/lib64/libgfortran.so.3.0.0
7f814069f000-7f81406a1000 rw-p 000ef000 08:02 4195479 /usr/lib64/libgfortran.so.3.0.0
7f81406a1000-7f81406a2000 rw-p 00000000 00:00 0
7f81406b2000-7f81406b5000 rw-p 00000000 00:00 0
7fffc7fc9000-7fffc7fde000 rw-p 00000000 00:00 0 [stack]
7fffc7fff000-7fffc8000000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Interestingly, the RMSDs are still printed out, but with some errors. Firstly, the RMSD with respect to the C-alpha atoms has some negative values. Secondly, all 3 RMSDs will have huge spikes, where the RMSD will go from something reasonable, like 3, to 200.
The first spike in the RMSDs occurs when at frame number 60 521. If I re-run ptraj reading in frames up to 60 520, I do not get any errors and all RMSDs are positive. Once I read in frame 60 521, I get the above errors.
To further attempt to isolate this problem, I obtained the pdb for frame 60521 from the trajectory, and some of the coordinates in this pdb are 0.000.
Does anyone have any clues as to what has gone wrong, and whether this is a problem with the simulation itself, or just in the ptraj analysis? Do you think the data generated up to frame 60 521 can be trusted, or the whole simulation must be discarded? Thank you for your help!
Sincerely,
Cassandra Churchill
PhD Student
Department of Chemistry
University of Alberta
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Received on Wed Feb 06 2013 - 10:30:03 PST
