HI,
I have generated three systems for the three SARS-CoV-2 glycosylated spike
proteins using CHARMM-gui to run MD simulation in AMBER 24. I have
generated separate parameters for each using amberFF14SB force field and
charmm36m force field, compatible to run in AMBER.
I tried to do minimization using amberFF14SB using the below input, but
there was a LINMIN failure with a message in the output file.
".... RESTARTED DUE TO LINMIN FAILURE ..."
Minimization input file in explicit solvent
&cntrl
! Minimization options
imin=1, ! Turn on minimization
maxcyc=25000, ! Maximum number of minimization cycles
ncyc=100, ! 100 steepest-descent steps, better for strained systems
! Potential energy function options
cut=12.0, ! nonbonded cutoff, in Angstroms
fswitch=10.0, ! Force-based switching
! Control how often information is printed to the output file
ntpr=100, ! Print energies every 100 steps
ntxo=2, ! Write NetCDF format
! Restraint options
ntr=1, ! Positional restraints for proteins, sugars, and ligands
nmropt=1, ! Dihedral restraints for sugars
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named WAT
owtnm='O', ! Water oxygens are named O
/
&ewald
vdwmeth = 0,
/
&wt
type='END'
/
DISANG=step4.0_minimization.rest
LISTIN=POUT
LISTOUT=POUT
&end
Protein posres
1.0
RES 1 1284 1285 2568 2569 3852
END
END
When I tried with "sander", it gave "segmentation fault".
Then I tried the charmm36m force field with the same input in AMBER. It
worked for two systems, but for the third system, charmm36m is giving
LINMIN failure.
Can someone suggest how to solve it?
Thanks
Sangita
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 03 2025 - 07:30:02 PST
