On Sat, Apr 25, 2015 at 11:37 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> 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?
>
Using the prmtop and inpcrd files you got from leap, run the following
command in ParmEd:
parmed.py -p pk.prmtop << EOF
loadRestrt pk.inpcrd
summary
EOF
What is the output of this command? I'm particularly interested in the
reported density. I've never actually solvated the way you did (i.e.,
explicitly setting the box dimensions), so I wonder if the PBC were not set
particularly well (an overly high density would explain your observations).
Also, I suggest using the "addIons" command *after* solvating, so that
water molecules are replaced by ions (or use "addIonsRand" instead, which
results in a more random ion distribution to start with).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 25 2015 - 14:00:04 PDT
