Analyzing the minimization output (the frames i obtained after the minimization), I realized that the 2 atoms involved in the previous error message belonged to the ligands and were not restrained during the minimization. Thus I changed this part in the minimization.in file:
Initial minimisation PknG-Adenine complex: minimization solvent + ions
&cntrl
imin=1,
maxcyc=1000,
ntb=1,
ntr=1,
cut=10,
restraint_wt = 10.0,
restraintmask=':1-246.CA,C,O,N | .3834-3848',
ntpr=1, ntwx=1, ntwr=100
Atoms from 3834 to 3848 are ligand's atoms (with H atoms).
I analyzed the output frames and the ligand was much more stable then before.
(The energy was flat and no overlaps were detected).
This structure was used as strating point for a short MD (to relax solvent molecules):
15ps MD PknG-Adenine complex: restraints on PknG-Ade residues while the solvent is leeting free
to relax
&cntrl
imin=0,
irest=0,
ntx=1,
ig=-1,
ntb=1,
ntr=1,
cut=10,
ntc=2,
ntf=2,
tempi=300.0,
temp0=300.0,
ntt=3,
gamma_ln=5.0,
nstlim=15000, dt=0.001,
ntpr=1, ntwx=1, ntwr=1000
restraint_wt = 10.0,
restraintmask=':1-246.CA,C,O,N | .3834-3848'
/
Sander stopped again at the begining:
vlimit exceeded for step 1; vmax = 82.0601
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 1923 3841 3848
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
If I restrained all ligand's atoms, why atoms 3841 and 3848 are still causing a problem?
Analizing the output file i saw a message related to the charge of the whole system:
Sum of charges from parm topology file = 0.00099988
Forcing neutrality...
Could it be a cause of my problem?
I ran the MD as:
sander -O -i PknGAde-wt-md.in -o PknGAde-wt-md.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde-wt-min.rst -r PknGAde-wt-md.rst -ref PknGAde-wt-min.rst -x PknGAde-wt-md.mdcrd &
Thus the set of initial coord and the ref coord are the same (both are the minimized structure), is it correct?
Vale
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Monday, May 12, 2014 4:18 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Analysis of minimization stage
On Mon, 2014-05-12 at 09:59 -0400, David A Case wrote:
> On Mon, May 12, 2014, Valentina Romano wrote:
> >
> > CPPTRAJ: Trajectory Analysis. V13.22
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> > AmberParm Title: [default_name]
> > Radius Set: modified Bondi radii (mbondi)
> > INPUT: Reading Input from file PknGAde-wt-min.check_overlap
> > [trajin PknGAde-wt-min.rst]
> > [PknGAde-wt-min.rst] contains 1 frames.
> > [checkoverlap]
>
> Try adding the "reportfile overlaps.dat" to the checkoverlap command.
> I'm always uncertain about when cpptraj writes things to stdout, and when
> they go to one of the data files.
Whenever I've used checkoverlaps before the report gets printed to
stdout...
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 12 2014 - 09:30:02 PDT
