Thanks for help, Hannes!
Yes, I turned off (ifsc=0) softcore treatment for "decharge state" and put
chargemask on second ligand softcore atoms. Do i need to turn this option
on (ifsc = 1)?
Also try minimize and heat at "lambda = 0.5, decharge" with the same effect
(blowing up).
About my system:
I have 3 carbon 6 hydrogen atoms in LTA region (MCS) and 5 softcore atoms.
All LTA atoms share same coordinates and have same order in pdb file.
PDB files looks like :
AAA.pdb
TITLE AAA
MODEL 1
HETATM 1 C1 AAA 900 -0.500 1.414 0.000 1.00 0.00
C
HETATM 2 C2 AAA 900 0.000 0.000 0.000 1.00 0.00
C
HETATM 3 C3 AAA 900 1.500 0.000 0.000 1.00 0.00
C
HETATM 4 H1 AAA 900 -1.590 1.414 0.000 1.00 0.00
H
HETATM 5 H2 AAA 900 -0.137 1.928 0.890 1.00 0.00
H
HETATM 6 H3 AAA 900 -0.137 1.928 -0.890 1.00 0.00
H
HETATM 7 H4 AAA 900 -0.363 -0.514 -0.890 1.00 0.00
H
HETATM 8 H6 AAA 900 1.863 0.514 0.890 1.00 0.00
H
HETATM 9 H7 AAA 900 1.863 0.514 -0.890 1.00 0.00
H
HETATM 10 C4 AAA 900 2.000 -1.414 0.000 1.00 0.00
C
HETATM 11 H8 AAA 900 3.090 -1.414 0.000 1.00 0.00
H
HETATM 12 H9 AAA 900 1.637 -1.928 0.890 1.00 0.00
H
HETATM 13 H10 AAA 900 1.637 -1.928 -0.890 1.00 0.00
H
HETATM 14 H5 AAA 900 -0.363 -0.514 0.890 1.00 0.00
H
ENDMDL
END
AAB.pdb
TITLE AAB
MODEL 1
HETATM 1 C1 UNK 900 -0.500 1.414 0.000 1.00 0.00
C
HETATM 2 C2 UNK 900 0.000 0.000 0.000 1.00 0.00
C
HETATM 3 C3 UNK 900 1.500 0.000 0.000 1.00 0.00
C
HETATM 4 H2 UNK 900 -1.590 1.414 0.000 1.00 0.00
H
HETATM 5 H3 UNK 900 -0.137 1.928 0.890 1.00 0.00
H
HETATM 6 H4 UNK 900 -0.137 1.928 -0.890 1.00 0.00
H
HETATM 7 H5 UNK 900 -0.363 -0.514 -0.890 1.00 0.00
H
HETATM 8 H6 UNK 900 1.863 0.514 0.890 1.00 0.00
H
HETATM 9 H7 UNK 900 1.863 0.514 -0.890 1.00 0.00
H
HETATM 10 C4 UNK 900 -0.509 -0.719 1.246 1.00 0.00
C
HETATM 11 H1 UNK 900 1.863 -1.028 0.000 1.00 0.00
H
HETATM 12 H8 UNK 900 -0.146 -1.747 1.246 1.00 0.00
H
HETATM 13 H9 UNK 900 -1.599 -0.719 1.246 1.00 0.00
H
HETATM 14 H10 UNK 900 -0.145 -0.206 2.136 1.00 0.00
H
ENDMDL
END
Thank you,
Artem
On Fri, Feb 24, 2017 at 7:47 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> On Fri, 24 Feb 2017 19:11:53 +0300
> Artem Shekhovtsov <job.shekhovtsov.gmail.com> wrote:
>
> > Hi! I have a problem with blowing system on relative free energy
> > calculation.
> > I finished tutorial A9 without problem and decided to try simulate
> > some simple system.
> > End states of simulation is n-butane and isobutane.
> > So I prepared starting files and parametrize molecules in antechamber.
> > I want to do main cycles (minimization -> heating -> pressuring ->
> > md) at each lambda point of simulation, not only at lambda = 0.5.
> > My system blew at "lambda = 0.05 decharge stage"
>
> Ah, right. That can be done with ifsc=0.
>
> Have you tried to minimize at, say, lambda=0.5 and use this structure
> to go into heating? Have you had success with any other nearby lambda
> and tried to start from that end structure?
>
>
> Cheers,
> Hannes.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 24 2017 - 11:30:03 PST
