Thanks you very much for all the time that you past to answer me.
I read all the mails that you send me. I tried all the suggestions that you advice me when I understand them and try to found a way to check the overlap with "checkoverlap" because it is not really explain in the manual.
I am really sorry if you feel that I don't take time to read your mail because it is not true. I am stuck with my problem and I really appreciate all your advice.
And of course I have a look of my system step by step. It is the first think that I ckeck.
So many thanks again for your help which was not a waste of time.
Regards,
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : mardi 25 février 2014 17:28
À : amber.ambermd.org
Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
Please look for overlapping atoms and actually visualize your system to
look for particle clashes. This has been suggested several times
previously and should always be the first step when debugging issues
such as these.
The minimization output also shows you the largest gradient (GMAX) on
any single atom. An example of one of my systems (which should be
fairly typical):
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.0746E+04 1.3729E+01 2.6279E+02 OD1 798
BOND = 263.6030 ANGLE = 532.5977 DIHED = 1188.6729
VDWAALS = 5072.8658 EEL = -62779.3044 HBOND = 0.0000
1-4 VDW = 630.2080 1-4 EEL = 4345.8461 RESTRAINT = 0.0000
The last step shows a significantly smaller gradient:
NSTEP ENERGY RMS GMAX NAME NUMBER
5000 -7.8506E+04 2.1858E-01 6.7570E+00 CG 240
BOND = 5634.4052 ANGLE = 264.1139 DIHED = 1165.0896
VDWAALS = 13601.2711 EEL = -103556.8382 HBOND = 0.0000
1-4 VDW = 388.8872 1-4 EEL = 3997.0573 RESTRAINT = 0.0000
You should be observing the same trends in your system. If your max
gradient is orders of magnitude greater than what you see in my system
at the end of the minimization, then there is probably an issue with
your starting geometry (which would hopefully be obvious if you checked
for overlaps and/or visualized the system with VMD or pymol).
Also telling is whether the gradient decreases during the course of the
minimization. If it's not, I suspect your box is far too small.
Another note is that leap will add a bounding box around the vdw
surfaces of each atom -- it will NOT create a 90x90x90 box unless the
starting atomic positions from packmol filled up the whole space. So
when you're computing the volume of the system you need to look at the
box dimensions at the bottom of the inpcrd file (NOT your packmol
input).
Ultimately these are just hints to help you diagnose what is wrong with
your starting structure (is it a problem in the box definition?
starting coordinates from packmol? etc.). You will have to be the one
to diagnose what went wrong since nobody else here has the files (or
likely the time) to inspect it themselves. This is all the help I can
offer for this issue.
Good luck,
Jason
P.S. Please read the full help emails and actually try the suggestions.
If you have tried them, acknowledge that and tell us what you found. I
find it irritating when I spend time to provide detailed help/tips and
it seems like you've only read a tiny part and not really _tried_ any of
the suggestions. I doubt I'm alone in this frustration.
On Tue, 2014-02-25 at 16:18 +0000, Mele N. wrote:
> 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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>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 10:00:04 PST
