Hello everyone,
I am trying to perform some membrane protein simulations using AMBER 10. I
have parallel version of Amber installed on a machine (2 dual core 2.33GHz
Intel processors, 8GB RAM and 500 GB hard disk). Amber installation was
fine, almost all test performed well and PASSED. I also tried parallel
AMBER runs on our test system and no problems, I was able to run it upto
all the 8 cores using sander.MPI, for example. Now, I am performing the
membrane protein simulations. The lipid membrane was generated, solvated,
added with ions using VMD. The protein and ligand system was immersed in
it. Finally, after a lot of work the *.inpcrd and *.prmtop files of the
whole system (ie protein, ligand, membrane, water and ions) were made. The
charges/parameters of lipids and ligand comes from ANTECHAMBER/am1bcc
methodology and all other parameters are standard ones from ff03.
Now I want to perform the energy minimisation of whole system:
I am using the command
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
mpirun -np 4 /usr/local/amber10/exe/sander.MPI -O -i minimise.in -o
minimise.out -c final_12S.inpcrd -p final_12S.prmtop -r final_12S.rst
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
It showed the following error:
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 3933 failed on node n0 (127.0.0.1) due to signal 11.
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
After checking the "minimise.out" file, I observed the following details in
it:
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 4.0063E+15 N 1792
BOND = 16082.1321 ANGLE = 10271.7354 DIHED = 9025.5857
VDWAALS = NaN EEL = NaN HBOND = 0.0000
1-4 VDW = 3502.0741 1-4 EEL = 27317.6570 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
250 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
300 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
350 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
400 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
450 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
550 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
600 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
650 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 2516779.8675 DIHED = 6890.4794
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
As it can be seen that van der Waals and Electrostatics are NaN here,
meaning there by that there are some serious atom-atom clashes. After
surfing this mailing list archive, I found out that the NUMBER mentioned
for the NSTEP = 1 in the "minimise.out" tells us about the atom making
clashing interactions with another atom. Thus, I loaded the structure in
VMD, checked the atom with index (=NUMBER - 1), and indeed this atom was
lying completely on top another one. Therefore, I altered the coordinates
of one of the atom and after trying again "this" atom clashing was gone,
but another one was there. Now NUMBER was 17436, I again altered the
coordinates and now this atom clashing was gone, but another one appeared.
It seems that VMD generated lipid+water+ion system contains some atom-atom
clashes, which needs to be removed to make it run now.
Please tell me, do I have to do it again and again untill there are no such
serious clashes (?). I saw few previous posts, yes, indeed it was mentioned
that nothing will proceed until the INITIAL structure does not contain any
such atom-over-atom situation.
Am I identifying the problem correctly here (?) OR do you think the error
(failure of minimisation) is because of some other reason (?)
Secondly, I think such a minimisation proceeds smoothly in NAMD, ie NAMD
minimizer is capable of performing minimisation without any errors. May be
it works fine, even when there is a serious clash among atoms. Does AMBER
has some parameter, which would enable me to run this minimisation
smoothly, to avoid removing many such clashes one-by-one. Please let me
know.
All your comments will help a lot.
thanks in advance,
Vivek
IMM, Pune.
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Received on Wed Apr 15 2009 - 01:08:01 PDT
