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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Received on Tue Nov 28 2017 - 03:30:02 PST
