On 1/10/10 9:47 PM, Jack Shultz wrote:
Thanks Justin,
I went back to the original pdb files. These were conformations of the
same protein derived from molecular dynamics simulations performed by
Andrey.
What I intially attempted was preping the structures using tleap, hoping
to paint in missing atoms for residues. Then use this to replace
Well, it seems that you may be hoping for too much :) Your log file shows a
whole bunch of failures that look to be related to some early processing of your
structure, and other warnings about close contacts detected in tleap.
I think you may need to start with an actual intact structure, or else coax your
preparation steps to make this happen. I am not too familiar with tleap and
sleap, do they magically fix missing atoms?
-Justin
non-standard residues
sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g fzd2_md7-8_c6_cc.pdb | sed s/PRO\ B\
\ \ 1/NPROB\ \ \ 1/g | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\
\ 99/CPHEB\ \ 99/g | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\
CPHE/OC2\ CPHE/g | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed
s/CYS\ /CYN\ /g > protein2.pdb
Then fixed the nterminal residue name. Finally replaced all CYS to CYS2
I went back and did the same thing except for tleap. It pdb2gmx seems to
process these files without needing the tleap step.
Still I see some of the same lincs errors.
rms 10.669050, max 173.182678 (between atoms 1857 and 1859)
rms 10.669803, max 173.177811 (between atoms 1857 and 1859)
rms 10.670179, max 173.175400 (between atoms 1857 and 1859)
rms 10.670368, max 173.174149 (between atoms 1857 and 1859)
rms 10.670460, max 173.173553 (between atoms 1857 and 1859)
rms 10.670508, max 173.173141 (between atoms 1857 and 1859)
rms 10.670531, max 173.173035 (between atoms 1857 and 1859)
rms 10.670543, max 173.172958 (between atoms 1857 and 1859)
rms 10.670549, max 173.172928 (between atoms 1857 and 1859)
rms 10.670552, max 173.172913 (between atoms 1857 and 1859)
rms 10.670554, max 173.172913 (between atoms 1857 and 1859)
rms 10.670554, max 173.172913 (between atoms 1857 and 1859)
ATOM 1857 CA HIE 120 43.362 28.084 25.727 1.00 0.00
ATOM 1858 HA HIE 120 43.677 27.135 25.748 1.00 0.00
ATOM 1859 CB HIE 120 42.112 28.226 24.788 1.00 0.00
also this atom consistently has a very high Fmax
Step= 3, Dmax= 1.4e-02 nm, Epot= 1.45860e+10 Fmax= 2.82224e+12,
atom= 19392
Step= 4, Dmax= 7.2e-03 nm, Epot= 1.45396e+10 Fmax= 2.82207e+12,
atom= 19392
Step= 5, Dmax= 3.6e-03 nm, Epot= 1.45106e+10 Fmax= 2.82194e+12,
atom= 19392
Step= 6, Dmax= 1.8e-03 nm, Epot= 1.44953e+10 Fmax= 2.82181e+12,
atom= 19392
Step= 7, Dmax= 9.0e-04 nm, Epot= 1.44887e+10 Fmax= 2.82196e+12,
atom= 19392
Step= 8, Dmax= 4.5e-04 nm, Epot= 1.44850e+10 Fmax= 2.82196e+12,
atom= 19392
Step= 9, Dmax= 2.2e-04 nm, Epot= 1.44832e+10 Fmax= 2.82196e+12,
atom= 19392
Step= 10, Dmax= 1.1e-04 nm, Epot= 1.44822e+10 Fmax= 2.82196e+12,
atom= 19392
Step= 11, Dmax= 5.6e-05 nm, Epot= 1.44818e+10 Fmax= 2.82196e+12,
atom= 19392
Step= 12, Dmax= 2.8e-05 nm, Epot= 1.44815e+10 Fmax= 2.82196e+12,
atom= 19392
Step= 13, Dmax= 1.4e-05 nm, Epot= 1.44814e+10 Fmax= 2.82196e+12,
atom= 19392
Its not clear to me what we should do to correct this structures...maybe
Andrey has some input.
http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun2.txt
On Sun, Jan 10, 2010 at 5:37 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
On 1/10/10 5:18 PM, Jack Shultz wrote:
I am trying to get this workflow opperational. However, my
systems are
getting unstable. I have preped two mdp files: 1) one for
restrained 2)
unrestrained. LINCS errors appear for restrained and
unrestrained has
infinite energy appearing.
http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_
<http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt>
__
This log file shows several "long bond" warnings, which may be the
root of your problem. See here:
http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms
Since your minimization is failing immediately, there is something
physically unreasonable about your structure, such that EM cannot
resolve the problem. Note, too, that one of the long bond warnings
pertained to atom 1668, which is the location of the first LINCS
warning. Coincidence? Not likely. Re-examine the starting
structure and figure out if anything is missing or poorly
reconstructed (e.g., from initially missing atoms).
This is where I get the LINCS Warnings
Step -1, time -0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.461520, max 14.428611 (between atoms 1668 and 1669)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Steepest Descents:
Tolerance (Fmax) = 1.00000e+04
Number of steps = 100
Warning: 1-4 interaction between 1658 and 1672 at distance 2.655
which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.09364e+09 Fmax= 2.21154e+11,
atom= 3292
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.680509, max 22.293625 (between atoms 1668 and 1670)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
What is a reasonable increase in table-extension. Is this a
mis-leading
suggestion?
You should not adjust the table-extension. The other part of the
error message is what you need to pay attention to ("your system is
exploding").
-Justin
Here is the log from the unrestrained minimization.
http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_
<http://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt>
Here is a zip archive containing the working directory for this
minimization. Its about 428 kb
http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip
--
Jack
http://drugdiscoveryathome.com <http://drugdiscoveryathome.com/>
http://hydrogenathome.org <http://hydrogenathome.org/>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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