Dear users,
I have prepared a system using following leap commands:
verbosity 2
loadamberparams frcmod.ionsjc_tip3p
mol=loadpdb pk_aligned.pdb
addions mol Na+ 0
solvatebox mol TIP3PBOX {30 30 45}
saveamberparm mol pk.prmtop pk.inpcrd
i minimized the structure, heated it to 300k and ran equilibration for 2
ns. At each step, i checked the structure for presence of any close
contacts using "check" command.
After minimization and heating, the system didn't report any close contacts
but after equilibration, i got a long list of close contacts (both between
solute-solvent and solvent-solvent) like this:-
--------------------------------------------------------------------
1 Warning: Atoms 4:C5_1.H5' and 66330:WAT_21868.H2 are close (0.67)
1 Warning: Atoms 13:C5_1.H6 and 20392:WAT_6556.O are close (0.34)
1 Warning: Atoms 13:C5_1.H6 and 20394:WAT_6556.H2 are close (0.69)
1 Warning: Atoms 30:G_2.P and 87424:WAT_28900.O are close (0.71)
1 Warning: Atoms 30:G_2.P and 87425:WAT_28900.H1 are close (0.26)
1 Warning: Atoms 37:G_2.C4' and 10084:WAT_3120.O are close (0.67)
1 Warning: Atoms 37:G_2.C4' and 10085:WAT_3120.H1 are close (0.63)
1 Warning: Atoms 42:G_2.N9 and 32186:WAT_10487.H1 are close (0.77)
1 Warning: Atoms 43:G_2.C8 and 32186:WAT_10487.H1 are close (0.58)
.
.
.
.
--------------------------------------------------------------------
What's going wrong here?
Thanks
Asmita
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Received on Sat Apr 25 2015 - 09:00:02 PDT
