hello,
Jason have already responded to your message. Did you read it ?
BTW, I think your box is too small, indeed
You have a box of 90*90*90=729000 A3 to fill a volume for 2437 water and 5560 dmso at ambient condition = 29.7*2437+131.51*5560= 803574.50 A3 (?)
Stephane
________________________________________
De : Mele N. [nm10g13.soton.ac.uk]
Envoyé : mardi 25 février 2014 17:18
À : AMBER Mailing List
Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
I want to create a box with 10% of water and 90% of dmso.
So for a box of 90*90*90 A if I want 90% of dmso it need 5560 molecule of dmso (density: 1.1g.cm-3 and M(dmso)=78.13g/mol)
And if I want 10% of water I need 2437 molecules of water (density :1g.cm-3, M(h2o)=18.01g/mol).
Tat why I applied this number in my packmol input file:
tolerance 2.0
filetype pdb
output box_mix.pdb
structure WATER.pdb
number 2437
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
I re compute my mixture box with packmol , I get same error:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 7343 57 59
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I think that the problem really came during the parametrization of my box with leap.
>From the output file that I get with packmol I did some modification:
Water:
- my water was named TIP3A , I change it by WAT
- the Oxygen of the water was caleed OH2 and I change it by O
DMSO:
- First from this website
http://q4md-forcefieldtools.org/REDDB/up/W-46/ I download the mol2 and the pdb file of the dmso. (tripos1.mol2, mol1.pdb)
- I use this to file in order to creat a lib and frcmod file of the dmso molecule
parmchk -i tripos .mol2 -f mol2 -o tripos1.frcmod
source leaprc.ff99SB
source leaprc.gaff
DMS = loadmol2 tripos1.mol2
saveoff DMS tripos1.lib
quit
- change DMSO by DMS
and I create my parameter and coordiante file for my mixture box:
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
Can you tell me if from this step I am completly wrong ?
Many thank,
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : mardi 25 février 2014 12:56
À : amber.ambermd.org
Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
On Tue, 2014-02-25 at 09:58 +0000, Mele N. wrote:
> Thanks a lot to take time to answer.
>
> I kept equilibration because I just copy past the same file and change parameter and forgot to change the name at the beginning by "heating".
> Actually my heating step doesn't work. It crashed at the beginning:
>
> vlimit exceeded for step 0; vmax = 54.5176
>
> 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.
>
> I had a look on my packmol input file and output file and I created a cubic box:
> This is my input file:
>
> 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
>
> Am I wrong in the way to build my box?
I don't know. If you know the experimental density of a 2:1 DMSO-water,
mixture you should be able to compute whether a 90x90x90 box is big
enough.
When I quickly calculated how many water molecules were necessary to
fill a 90x90x90 A box to achieve a density of 1 g/mL, I got ~24000 water
molecules (which is far fewer than the 2684 water molecules plus 5560
DMSO molecules you added). Have you visualized your system?
I strongly encourage you to use the "checkoverlap" command in cpptraj to
see if you have overlapping solvent molecules. It's also always helpful
to visualize your system and see if you can find any obvious problems.
This looks to me like you have steric clashes so strong that not even
minimizations can solve it.
You can look at the maximum gradient printed at the end of your
minimization output file to see where clashes might be occurring. I
still think there is a problem with your box definition leading to the
clashes. Check that the resulting volume you get by multiplying the box
edge lengths matches what you expect based on your packmol input.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 09:00:06 PST
