Hi dear Jason,
thanks a lot.
I will search.
Regards
2015-05-14 12:16 GMT-05:00 Jason Swails <jason.swails.gmail.com>:
> On Thu, May 14, 2015 at 10:26 AM, Carlos Romero <carlos.rom.74he.gmail.com
> >
> wrote:
>
> > HI dear all.
> >
> > I am tryin to minimize a complex (p2y12-ADP).
> > I followed the next procedure:
> >
> > in tleap:
> > loadamberprep ADP.prep
> > loadamberparams frcmod.phos
> > p2y = loadpdb p2y12_Complex_adp.pdb
> > loadamberparams frcmod.ionsjc_jc_tip3p
> > addions py2 Cl- 0
> > solvatebox p2y TIP3PBOX 8.0
> > saveamberparm p2y p2y_adp.prmtop p2y_adp.inpcrd
> >
> > (I used HEX 6.3 for docking p2y12-ADP).
> >
> > my min.in is as amber`s tutorial
> >
> > minimise ras-raf
> > &cntrl
> > imin=1,maxcyc=1000,ncyc=500,
> > cut=8.0,ntb=1,
> > ntc=2,ntf=2,
> > ntpr=100,
> > ntr=1, restraintmask=':1-356',
> > restraint_wt=2.0
> > /
> >
> >
> > but i got the nest message:
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 300 -1.2037E+05 1.3465E+01 5.0121E+01 O 32200
> >
> > BOND = 1552.2692 ANGLE = 1423.1543 DIHED =
> > 4418.9944
> > VDWAALS = 5630.6523 EEL = -146087.8318 HBOND =
> > 0.0000
> > 1-4 VDW = 893.2273 1-4 EEL = 11764.0637 RESTRAINT =
> > 39.9951
> > EAMBER = -120405.4706
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 400 -1.2037E+05 1.3465E+01 5.0121E+01 O 32200
> >
> > BOND = 1552.2693 ANGLE = 1423.1536 DIHED =
> > 4418.9942
> > VDWAALS = 5630.6378 EEL = -146087.8061 HBOND =
> > 0.0000
> > 1-4 VDW = 893.2277 1-4 EEL = 11764.0643 RESTRAINT =
> > 39.9953
> > EAMBER = -120405.4591
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 500 -1.2037E+05 1.3465E+01 5.0121E+01 O 32200
> >
> > BOND = 1552.2695 ANGLE = 1423.1528 DIHED =
> > 4418.9941
> > VDWAALS = 5630.6253 EEL = -146087.7831 HBOND =
> > 0.0000
> > 1-4 VDW = 893.2280 1-4 EEL = 11764.0651 RESTRAINT =
> > 39.9955
> > EAMBER = -120405.4482
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 600 -1.2037E+05 1.3465E+01 5.0121E+01 O 32200
> >
> > BOND = 1552.2695 ANGLE = 1423.1526 DIHED =
> > 4418.9941
> > VDWAALS = 5630.6218 EEL = -146087.7760 HBOND =
> > 0.0000
> > 1-4 VDW = 893.2281 1-4 EEL = 11764.0654 RESTRAINT =
> > 39.9955
> > EAMBER = -120405.4445
> >
> > ... RESTARTED DUE TO LINMIN FAILURE ...
> >
> > ***** REPEATED LINMIN FAILURE *****
> >
> > ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO
> > *****
> >
>
> Did you click on this link?
>
> I have checked my pdb file adn everything looks fine.
> >
> > Does somebody have any suggestion?
> >
>
> Click on the above link and/or google "LINMIN FAILURE amber".
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu May 14 2015 - 12:00:02 PDT
