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 *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
614 -1.2037E+05 1.3465E+01 5.0121E+01 O 32200
BOND = 1552.2695 ANGLE = 1423.1526 DIHED =
4418.9941
VDWAALS = 5630.6213 EEL = -146087.7751 HBOND =
0.0000
1-4 VDW = 893.2281 1-4 EEL = 11764.0655 RESTRAINT =
39.9955
EAMBER = -120405.4441
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.07 ( 0.02% of Total)
| Build the list 1.19 (78.63% of List )
| Other 0.32 (21.37% of List )
| List time 1.52 ( 0.40% of Nonbo)
| Short_ene time 289.75 (98.46% of Direc)
| Other 4.52 ( 1.54% of Direc)
| Direct Ewald time 294.27 (77.10% of Ewald)
| Adjust Ewald time 3.97 ( 1.04% of Ewald)
| Fill Bspline coeffs 3.46 ( 4.19% of Recip)
| Fill charge grid 10.80 (13.10% of Recip)
| Scalar sum 15.35 (18.62% of Recip)
| Grad sum 21.16 (25.66% of Recip)
| FFT time 31.69 (38.43% of Recip)
| Recip Ewald time 82.46 (21.61% of Ewald)
| Virial junk 0.22 ( 0.06% of Ewald)
| Other 0.74 ( 0.19% of Ewald)
| Ewald time 381.66 (99.60% of Nonbo)
| Nonbond force 383.18 (97.70% of Force)
| Bond/Angle/Dihedral 8.90 ( 2.27% of Force)
| Other 0.13 ( 0.03% of Force)
| Force time 392.21 (100.0% of Runmd)
| Runmd Time 392.21 (98.97% of Total)
| Other 4.01 ( 1.01% of Total)
| Total time 396.29 (100.0% of ALL )
| Highest rstack allocated: 2427876
| Highest istack allocated: 44886
| Job began at 09:07:43.775 on 05/14/2015
| Setup done at 09:07:44.593 on 05/14/2015
| Run done at 09:14:20.066 on 05/14/2015
| wallclock() was called 23384 times
I have checked my pdb file adn everything looks fine.
Does somebody have any suggestion?
Thanks in advance.
Regards
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Received on Thu May 14 2015 - 07:30:03 PDT
