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 - 10:30:03 PDT
