On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
Another thing worth considering - why do you necessarily need the rest of the
structure to be identical? Or perhaps better stated, why do you believe this to
be the more appropriate model of reality? Phosphorylation events frequently
trigger structural changes in the protein, so I see no reason to assume it will
have no effect on the rest of the structure. At the very least, you can try a
"normal" EM and MD procedure without freezing anything to see if you can
determine the problem. If things run normally without freezing, then you know
that whatever you are doing here is artificial and problematic.
-Justin
I just added the phosphate manually and so I want to minimize and run a
short MD with it.
I added the dihedraltype of the amber database
(http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
to the ffbonded file.
And additionally I looked at the protein and made all the residues which
could somehow influence the protein flexible so that eventual clashes can
be repaired.
But still I got the error:
..Step 3612, time 3.612 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000008, max 0.000031 (between atoms 975 and 978)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
976 979 32.6 0.0961 0.0960 0.0960
Step 3613, time 3.613 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000237, max 0.001400 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
976 979 33.4 0.0960 0.0959 0.0960
..
Too many LINCS warnings (1000)
I already minimized the protein and everything was fine. There were no
errors:
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -7.7436938e+05
Maximum force = 8.6871973e+03 on atom 979
Norm of force = 7.1224258e+01
gcq#49: "You Could Make More Money As a Butcher" (F. Zappa)
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -7.7436938e+05
Maximum force = 8.6871973e+03 on atom 979
Norm of force = 7.1224258e+01
And also during the grompp run there are no errors.
Can you please help me to find out where the problem lies?
Thank you,
Eva
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah okey. Thank you.
I will write them.
Hmm, but the protein is a crystal structure from pdb with a resolution
of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the minimized structure. So I thought
that I only had to minimize the phosphate and the residue it bound on.
Or is there a mistake in my thought here?
If adding the phosphate resulted in a crash, then clearly that's the
problem. I
don't understand why you would run EM on just the phosphate and keep the
rest of
the protein structure frozen. Again, that potentially prevents clashes
from
being resolved. I don't understand what value there is in only minimizing
the
phosphate.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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