________________________________________
De : David A Case [case.biomaps.rutgers.edu]
Envoyé : lundi 24 février 2014 18:32
À : AMBER Mailing List
Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
On Mon, Feb 24, 2014, Mele N. wrote:
> - first I tried to turn on shake during minimization but the
> minimization crash with the same error:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
>
> - after this error I run a new minimization without shake and no problem.
How about trying an additional minimization with shake, starting from the
output of the first minimization? If these still have SHAKE failures, your
MD runs are all likely to fail as well.
Jason's suggestions about checking the box info are also good ones.
...dac
I trying second minimization with shake and it doesn t work:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 35579 45871 45873
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
*** Especially for minimization, try ntc=1 (no shake)
I answer to jason. With packmol I created a cubic mixture box and I set this box into Leap:
tolerance 2.0
filetype pdb
output box_mix.pdb
structure WATER.pdb
number 2684
inside box 0. 0. 0. 90. 90. 90.
end structure
structure dmso.pdb
number 5560
inside box 0. 0. 0. 90. 90. 90.
end structure
And this is the input file from leap:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams tripos1.frcmod
loadoff tripos1.lib
MOL = loadpdb box_mix.pdb
setbox MOL vdw
saveamberparm MOL mix.prmtop mix.inpcrd
savepdb MOL box_leap.pdb
quit
It may be a problem at this step but I have no idea what I did wrong. I parameterized my dmso compound into leap in order to create a library and frcmod file and from that I created my parameter and coordinate file from leap for my mixture box.
Thanks a lot for your help.
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Received on Tue Feb 25 2014 - 03:00:02 PST
