On Fri, Mar 08, 2019, Zhonghua Xia wrote:
>Initial minimisation with Cartesian restrains for the solvent (hold the protein and Cl-)
> &cntrl
> imin=1, maxcyc=3000,
> ntr=1,
> restraint_wt=100,
> restraintmask=':1-90'
> &end
Set ntpr=1 to get more detailed output. Also, you can use the "check"
command in cpptraj to analyze your system for bad contacts.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.3472E+08 2.4011E+02 1.9793E+04 C 1441
>
> BOND = 9784.2491 ANGLE = 1786.4015 DIHED = 934.9579
> VDWAALS = ************* EEL = -62579.0562 HBOND = 0.0000
> 1-4 VDW = 1083.6816 1-4 EEL = 4202.4250 RESTRAINT = 0.0000
Still, it's a bit unusual that an initial energy of "only" 4 x 10^8
won't minimize away. Try reducing your restraint weight by at least a
factor of 10. If the bad contact is in residues 1-90, then your
powerful restraints are forcing those atoms to stay where they are.
Hence you may have to two very strong and competing energy terms, one
trying to relieve a bond contact and another trying to keep it in place.
...good luck...dac
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Received on Fri Mar 08 2019 - 06:30:04 PST
