Dear Vaibhav,
Yes, you should consider increasing the number of minimization steps for large systems (e.g. it took me more than 20000 steps the proper minimization of a virus). This will of course depend on the former resolution and scoring (e.g. wwPDB Validation) of your initial structure.
Also consider an additional step of full minimization, without restraining the backbone.
Also consider playing with the keyword "ncyc" to alternate between steepest-descent and conjugate-gradient algorithms... the first is good for fast fixing "large issues" but has very slow convergence for solving fine problems...
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 26 de Junio 2019 11:48:24
Asunto: [AMBER] how to check if bad contacts exsist after min heat jobs
Dear All,
I ran min job on a protein with > 500 residues with 10000 cycles of
minimization.
But this structure crashes in the heating job.
The min.rst7 still has close contacts (when I created a pdb and loaded back
in leap).
Is there a faster way to check structures after min, heat jobs to ensure if
they are ok for the next steps in MD simulations?
I am assuming that for larger proteins additional step of min, heat, equil
will be required.
Can you please guide in this direction on how to set-up such calculations,
potential pitfalls to observe for and any general corrective steps to take?
I'm guessing E, temp, presence of close contacts should be monitored. Are
there any other things to ensure (like water distributions/density, or
something else, not sure how to check this?)
Please point to existing Ambertools-specific tutorials, articles, reviews
that might help here.
My apologies, if this ends up being a trivial matter.
[xxxxxx.hlogin1 rup-xxx-implicit]$ more min.in
Minimization to prepare for constant pH MD
&cntrl
imin = 1, ! Turn on minimization
igb = 2, ! Use the GB model CpHMD was parametrized for
saltcon = 0.1, ! Use the salt conc. CpHMD was parametrized
for
maxcyc = 10000, ! Total number of minimization cycles
icnstph = 1, ! Turn on constant pH
ntcnstph = 100000, ! Never attempt to change prot. states
cut = 1000.0, ! No cutoff
ntr = 1, ! Turn on positional restraints
restraint_wt = 10, ! 10 kcal/mol/A**2 restraint force constant
restraintmask = '.CA,C,O,N' ! Restraints on the backbone atoms only
/
Warning: One sided connection. Residue (default_name) missing connect1 atom.
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NB-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NA-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-ND-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NC-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 7806
> check 1W0E
Checking '1W0E'....
Warning: The unperturbed charge of the unit (2.000998) is not zero.
Warning: Close contact of 1.083725 angstroms between .R<ARG 81>.A<HH21 21>
and .R<GL4 349>.A<HE21 14>
Warning: Close contact of 0.980098 angstroms between .R<ARG 81>.A<HE 15>
and .R<GL4 349>.A<HE11 18>
Warning: Close contact of 1.267602 angstroms between .R<TYR 154>.A<HH 15>
and .R<VAL 158>.A<HG22 13>
Warning: Close contact of 1.251913 angstroms between .R<ILE 159>.A<HG23 10>
and .R<SER 163>.A<HG 9>
Checking parameters for unit '1W0E'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 5
Unit is OK.
thank you.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
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Received on Wed Jun 26 2019 - 12:00:03 PDT
