Hi David and Amber users
I did two-step minimization. In the first step I keep the heavy atoms fixed
and minimized solvent and in the second step, I did minimization for the
complete system. In both I get error of ***** REPEATED LINMIN FAILURE
*****.
*For the first step minimization input and result is as follows:-*
Minimization with Cartesian restraints for the solute
&cntrl
imin=1, maxcyc=100000,
ntmin=1, ncyc= 1000,
ntpr=5,
ntr=1,
&end
Group input for restrained atoms
100.0
RES 1 491
END
END
27735 -2.7469E+05 9.3928E-03 1.8648E+00 CG 3759
BOND = 21121.9343 ANGLE = 1047.6745 DIHED =
6126.8150
VDWAALS = 50817.5947 EEL = -374077.1085 HBOND =
0.0000
1-4 VDW = 2103.1482 1-4 EEL = 18037.6420 RESTRAINT =
129.8722
EAMBER = -274822.2997
NSTEP ENERGY RMS GMAX NAME NUMBER
27740 -2.7469E+05 9.3699E-03 1.8599E+00 CG 3759
BOND = 21121.9343 ANGLE = 1047.6745 DIHED =
6126.8150
VDWAALS = 50817.5949 EEL = -374077.1088 HBOND =
0.0000
1-4 VDW = 2103.1482 1-4 EEL = 18037.6421 RESTRAINT =
129.8722
EAMBER = -274822.2998
NSTEP ENERGY RMS GMAX NAME NUMBER
27745 -2.7469E+05 9.3683E-03 1.8595E+00 CG 3759
BOND = 21121.9343 ANGLE = 1047.6745 DIHED =
6126.8150
VDWAALS = 50817.5949 EEL = -374077.1088 HBOND =
0.0000
1-4 VDW = 2103.1482 1-4 EEL = 18037.6421 RESTRAINT =
129.8722
EAMBER = -274822.2998
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
*For the second step minimization input and result is as follows:-*
Minimization of the entire molecular system
&cntrl
imin=1, maxcyc=50000,
ntpr=5,
&end
NSTEP ENERGY RMS GMAX NAME NUMBER
29640 -2.7917E+05 4.5493E-03 2.9666E-01 H1 44506
BOND = 21276.6440 ANGLE = 1174.1935 DIHED =
5770.7288
VDWAALS = 50844.8463 EEL = -377356.3823 HBOND =
0.0000
1-4 VDW = 1606.3203 1-4 EEL = 17510.6896 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
29645 -2.7917E+05 4.5456E-03 2.9654E-01 H1 44506
BOND = 21276.6441 ANGLE = 1174.1935 DIHED =
5770.7288
VDWAALS = 50844.8463 EEL = -377356.3825 HBOND =
0.0000
1-4 VDW = 1606.3203 1-4 EEL = 17510.6896 RESTRAINT =
0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
29649 -2.7917E+05 4.5456E-03 2.9654E-01 H1 44506
BOND = 21276.6441 ANGLE = 1174.1935 DIHED =
5770.7288
VDWAALS = 50844.8463 EEL = -377356.3825 HBOND =
0.0000
1-4 VDW = 1606.3203 1-4 EEL = 17510.6896 RESTRAINT =
0.0000
***** REPEATED LINMIN FAILURE *****
*I did checkvalidity also in parmed and it says prmtop is ok*
parmed complex.prmtop
_~__________________
|_|_______________|_|
| ,-------------. |
| | .---------. | |
| | |P | | |
| | | a | | |
| | | r | | |
| | | m ED | | |
| | `---------' | |
| `---------------' |
| _ ParmedBoy |
| _| |_ ,-. |
||_ O _| ,-. "._,"|
| |_| "._," A |
| _ _ B |
| // // |
| // // \\\\\\ |
| ` ` \\\\\\ ,
|________...______,"
ParmEd: a Parameter file Editor
Loaded Amber topology file complex.prmtop
Reading input from STDIN...
> checkValidity
Determining validity of prmtop
*complex.prmtop looks OK to me!> *
What should I do to fix this error? Need your suggestions, please.
Sadaf
On Wed, Aug 21, 2019 at 3:13 AM David Case <david.case.rutgers.edu> wrote:
> On Tue, Aug 20, 2019, Sadaf Rani wrote:
>
> >I am running equilibration of protein-ligand complex system
> >vlimit exceeded for step 0; vmax = 1751.7001
>
> This implies that your starting structure has bad forces, even at the
> first step. Have you run a minimization before this?
>
> You can also use the checkValidity action (in parmed) or the
> checkStructure action (in cpptraj) to look for common problems.
>
> >
> > Coordinate resetting cannot be accomplished,
> > deviation is too large
> > iter_cnt, my_bond_idx, i and j are : 1 24 7053 7052
>
> Atoms 7053 and 7052 are (at least) one place where there are problems.
> You could look at these areas (say with a visualization program) to see
> if you can spot the problem. But somehow, you need a better starting
> structure. Minimization will usually, but not always, provide this.
>
> ....dac
>
>
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Received on Wed Aug 21 2019 - 02:30:02 PDT
