thank you sir.
On Tue, Nov 28, 2017 at 4:10 PM, Marcelo Andrade Chagas <
andrade.mchagas.gmail.com> wrote:
> Dear,
>
> try performing the minimization in steps,
>
> for example, by first minimizing water molecules,
> then the protein with some restrictions and finally the whole system
> no restrictions. Talves can be malicious and / or overlapping
> of waste that is causing electrostatic energy to go to values
> very high, so it does not appear there.
>
> follows an example.
>
> Best regards
>
> ____________________________________________________________________
> Minimize
> &cntrl
> imin=1,
> ntx=1,
> irest=0,
> maxcyc=5000,
> ncyc=1000,
> ntpr=100,
> ntb=0,
> igb=1,
> ntwx=0,
> ntr=1,
> restraint_wt=100.0,
> restraintmask=":1-332",
> cut=10.0
> /
>
> ___________________________________________________________________
> Minimize
> &cntrl
> imin=1,
> ntx=1,
> irest=0,
> maxcyc=5000,
> ncyc=1000,
> ntpr=100,
> ntb=0,
> igb=1,
> ntwx=0,
> ntr=1,
> restraint_wt=100.0,
> restraintmask=":21,23,135,167,196,267,330,331,332",
> cut=10.0
> /
> _______________________________________________________________________
> Minimize
> &cntrl
> imin=1,
> ntx=1,
> irest=0,
> maxcyc=5000,
> ncyc=1000,
> ntpr=100,
> ntb=0,
> igb=1,
> ntwx=0,
> ntr=0,
> cut=10.0
> /
> _______________________________________________________________________
>
>
>
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2017-11-28 9:01 GMT-02:00 Rana Rehan Khalid <rrkhalid.umich.edu>:
>
> > Dear All
> >
> > I want to minimize the structure but when simulation start the values of
> > VDWAALS not show. is it due to poor starting structure or structure have
> > more clashes. KIndly tell hoe i can remove the clashes through MD
> > simulation. Regards
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 3.3484E+18 9.6235E+17 4.9465E+20 C 6484
> >
> > BOND = 5320.4918 ANGLE = 24456.6551 DIHED =
> > 20708.3171
> > VDWAALS = ************* EEL = -645997.9707 HBOND =
> > 0.0000
> > 1-4 VDW = ************* 1-4 EEL = 56119.7849 RESTRAINT =
> > 0.0000
> >
> > thanks
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Nov 28 2017 - 03:30:03 PST
