Date: Mon, 2 Nov 2015 18:28:37 +0100
Dear Jason
thanks a lot for your kind email.
Since my peptide is chimeric initially I have many bad contact created
problems, so to remove bad contacts I performed on linear structure VACUUM
simulation just to get a starting structure free from bad contact.
Eventually I am going to use restraints to fold my molecule. Then after
folding it in vacuum, I was planing to refinement it in explicit solvent.
I followed this tutorial http://ambermd.org/tutorials/advanced/tutorial4/,
where they folded the dna in vaccum (with restraint) and for the final
touch they performed NMR refinement in implicit solvent (GB) not in
explicit solvent.
To your suggestion, I did follow internet to deal with my situation but I
never find a answer to start directly calculation from the water itself.
Since my goal was to use water but in the final touch. Unfortunately there
is no script to perform simulated annealing in explicit solvent. I found in
two paper following this methods (image below).
In this paper when, they mentioned best structure by default I understood
that from vacuum. Again they don't report the script for explicit solvent
so that I can adopt. (image below)
But for best structure (vocum) just now I performed GB (script attached)
and calculations runs fine. Since I am using vacuum annealing script for
explicit solvent, may be this is the problem
GB annealing output
============================
NSTEP = 0 TIME(PS) = 4918.000 TEMP(K) = 19.78 PRESS =
0.0
Etot = -3360.1684 EKtot = 27.8925 EPtot =
-3388.0609
BOND = 70.9813 ANGLE = 286.5994 DIHED =
450.8731
1-4 NB = 117.4511 1-4 EEL = 327.2327 VDWAALS =
162.3998
EELEC = -4043.3678 EGB = -985.5726 RESTRAINT =
225.3422
EAMBER (non-restraint) = -3613.4031
------------------------------------------------------------------------------
NMR restraints: Bond = 225.342 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 200 TIME(PS) = 4918.200 TEMP(K) = 331.54 PRESS =
0.0
Etot = -2920.2706 EKtot = 467.4367 EPtot =
-3387.7073
BOND = 103.8310 ANGLE = 286.2567 DIHED =
352.3046
1-4 NB = 88.1125 1-4 EEL = 315.5648 VDWAALS =
-107.5209
EELEC = -2847.8648 EGB = -2094.4195 RESTRAINT =
516.0284
EAMBER (non-restraint) = -3903.7357
------------------------------------------------------------------------------
NMR restraints: Bond = 516.028 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 400 TIME(PS) = 4918.400 TEMP(K) = 413.46 PRESS =
0.0
Etot = -2565.0493 EKtot = 582.9372 EPtot =
-3147.9865
BOND = 129.4628 ANGLE = 304.8040 DIHED =
341.6718
1-4 NB = 89.8825 1-4 EEL = 308.3265 VDWAALS =
-103.3412
EELEC = -1517.3602 EGB = -3420.2096 RESTRAINT =
718.7769
EAMBER (non-restraint) = -3866.7635
------------------------------------------------------------------------------
NMR restraints: Bond = 718.777 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 600 TIME(PS) = 4918.600 TEMP(K) = 534.91 PRESS =
0.0
Etot = -2292.1147 EKtot = 754.1753 EPtot =
-3046.2899
BOND = 145.4071 ANGLE = 345.7286 DIHED =
373.0538
1-4 NB = 98.9978 1-4 EEL = 328.6083 VDWAALS =
-80.4866
EELEC = -398.8029 EGB = -4557.0747 RESTRAINT =
698.2786
EAMBER (non-restraint) = -3744.5686
------------------------------------------------------------------------------
[image: Inline images 1]
[image: Inline images 2]
I kindly request your inputs
thanks a lot
Vince
On 2 November 2015 at 17:49, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Nov 2, 2015 at 10:12 AM, V. Kumar <vin.vasanth.gmail.com> wrote:
>
> > Dear Carlos
> >
> > thank you so much for your kind response.
> >
> > I have a modified peptide(zinc finger domain). I have constructed my
> force
> > field files to handle these modification in amber. Then I performed 10ns
> MD
> > simulation vacuum. From the MD simulation I have extracted the low energy
> > structure(LES). I have used LES.pdb to convert the NMR restraints
> > (CYANA/DYANA format) in to amber format. Then I performed both 20 and
> 200ps
> > simulated annealing in vacuum (with restraints). Everything went nice,
> > there was no vlimt error (output below). I got expected structure (close
> to
> > 70%).
>
>
> >
> > In the next step I took a best structure from the above simulated
> annealing
> > protocol and solvated it 10A° TIP3PBOX.
>
>
> I would recommend against using this recipe. Vacuum dynamics are MUCH
> different than dynamics in the solution phase, and standard Amber
> parameters have been heavily trained for use in solution, not vacuum. I
> would personally suggest doing the entire system setup and preparation in
> the same explicit solvent you plan on using for the whole simulation, but
> at the very least you should use a GB potential in the first steps to
> incorporate *some* solvation effects.
>
>
>
> > Again to perform restrained
> > molecular dynamics (rMD)
> > I have constructed solvated.prmtop and solvated.inpcrd file from the best
> > structure(from vacuum rMD). With these two new file I performed the rMD
> as
> > in the same way as vacuum rMD. During this I stated to see vlimit
> exceeded
> > for steps.
> >
>
> My main argument here is that "best vacuum structure" may be completely
> unrelated to realistic solution phase structures. After all, water plays a
> *critical* role in stabilizing the native folds of most proteins. Without
> water, the native states of proteins are likely *very* different from what
> they are in solution, so preparing a system in vacuum may be making your
> starting structure significantly worse than not preparing it at all...
>
> Furthermore, once you add solvent to your structure, you need to minimize
> again. The vlimit errors are likely caused by close contacts between atoms
> that are introducing large forces and, as a result, integration errors.
>
> Another common mistake when using restraints is to have the wrong starting
> value for the restraints so that the restraint force is incredibly large
> (which can lead to vlimit errors and system blowups). That doesn't really
> look like what's happening based on your output, but I also don't know how
> many restraints you have defined for your system.
>
> HTH,
> Jason
>
>
> > here is a bit of it: vlimit exceeded for step 2941; vmax = 11.2167
> >
> >
> > from Vacuum to TIP3PBOX I have followed the same procedure, except for
> > TIP3PBOX, I took nest structure from vacuum to construct
> > solvate.prmtop/.inpcrd file.
> >
> >
> > I have attached the anneal.in script that I have used for both vacuum
> and
> > TIP3PBOX rMD
> >
> >
> > To eliminated the vlimt problem, first I have performed minimization1
> > (holding peptide and water is free ), minimization2 (all peptide+water)
> > followed by equilibrium 1 2 3.
> >
> > Then for simulated annealing (rMD) I have used eqil.rst file instead of
> > using solvate.inpcrd file. But still is showing vlimit cross. I dont know
> > it is common, this is first time I am doing simulation your in put is
> > highly appreciated.
> >
> > output file vacuum simulated annealing
> > ============================
> >
> >
> > eedmeth=5: Using 1/r dielectric
> >
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST = 95396
> > | TOTAL SIZE OF NONBOND LIST = 95396
> >
> > NSTEP = 0 TIME(PS) = 4918.000 TEMP(K) = 19.78 PRESS =
> > 0.0
> > Etot = -429.4810 EKtot = 27.8925 EPtot =
> > -457.3735
> > BOND = 70.9813 ANGLE = 286.5994 DIHED =
> > 450.8731
> > 1-4 NB = 117.4511 1-4 EEL = 10.5509 VDWAALS =
> > 161.4266
> > EELEC = -1780.5981 EHBOND = 0.0000 RESTRAINT =
> > 225.3422
> > EAMBER (non-restraint) = -682.7157
> >
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 225.342 Angle = 0.000 Torsion =
> 0.000
> >
> >
> ===============================================================================
> >
> > NSTEP = 200 TIME(PS) = 4918.200 TEMP(K) = 247.48 PRESS =
> > 0.0
> > Etot = -105.0733 EKtot = 348.9205 EPtot =
> > -453.9938
> > BOND = 102.6521 ANGLE = 306.9077 DIHED =
> > 347.5186
> > 1-4 NB = 93.7027 1-4 EEL = 17.3353 VDWAALS =
> > 82.4248
> > EELEC = -1767.7209 EHBOND = 0.0000 RESTRAINT =
> > 363.1859
> > EAMBER (non-restraint) = -817.1797
> >
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 363.186 Angle = 0.000 Torsion =
> 0.000
> >
> >
> ===============================================================================
> >
> > NSTEP = 400 TIME(PS) = 4918.400 TEMP(K) = 305.40 PRESS =
> > 0.0
> > Etot = 144.4193 EKtot = 430.5842 EPtot =
> > -286.1650
> > BOND = 115.4220 ANGLE = 311.4444 DIHED =
> > 364.1024
> > 1-4 NB = 99.3136 1-4 EEL = 3.6630 VDWAALS =
> > 84.7800
> > EELEC = -1682.8014 EHBOND = 0.0000 RESTRAINT =
> > 417.9111
> > EAMBER (non-restraint) = -704.0761
> >
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 417.911 Angle = 0.000 Torsion =
> 0.000
> >
> >
> ===============================================================================
> >
> >
> >
> > output file TIP3PBOX simulated annealing
> > ===============================
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 11.03 PRESS =
> > 0.0
> > Etot = -59890.8057 EKtot = 649.6399 EPtot =
> > -60540.4456
> > BOND = 71.6937 ANGLE = 639.4972 DIHED =
> > 472.2437
> > 1-4 NB = 794.5605 1-4 EEL = 34.3754 VDWAALS =
> > 6864.8488
> > EELEC = -69518.3437 EHBOND = 0.0000 RESTRAINT =
> > 100.6789
> > EAMBER (non-restraint) = -60641.1245
> >
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 100.679 Angle = 0.000 Torsion =
> 0.000
> >
> >
> ===============================================================================
> > vlimit exceeded for step 0; vmax = 95.6846
> > vlimit exceeded for step 1; vmax = 15.4126
> > vlimit exceeded for step 3; vmax = 11.7073
> > vlimit exceeded for step 5; vmax = 15.1512
> > vlimit exceeded for step 11; vmax = 10.2301
> > vlimit exceeded for step 12; vmax = 11.6621
> > vlimit exceeded for step 13; vmax = 11.0574
> > vlimit exceeded for step 14; vmax = 10.6736
> > vlimit exceeded for step 26; vmax = 10.0459
> > vlimit exceeded for step 27; vmax = 12.0479
> > vlimit exceeded for step 28; vmax = 11.6578
> > vlimit exceeded for step 29; vmax = 10.9358
> > vlimit exceeded for step 43; vmax = 10.1884
> > vlimit exceeded for step 44; vmax = 10.4415
> > vlimit exceeded for step 73; vmax = 10.7086
> > vlimit exceeded for step 103; vmax = 10.0620
> > vlimit exceeded for step 183; vmax = 25.0547
> > vlimit exceeded for step 184; vmax = 2276.3207
> > vlimit exceeded for step 185; vmax = 22.6012
> > vlimit exceeded for step 186; vmax = 23.5286
> > vlimit exceeded for step 187; vmax = 27.1868
> > vlimit exceeded for step 188; vmax = 23.6389
> > vlimit exceeded for step 189; vmax = 14.3901
> > vlimit exceeded for step 190; vmax = 12.2346
> > vlimit exceeded for step 191; vmax = 23.0398
> > vlimit exceeded for step 192; vmax = 15.8632
> > vlimit exceeded for step 193; vmax = 10.5260
> > vlimit exceeded for step 196; vmax = 10.3742
> >
> > NSTEP = 200 TIME(PS) = 0.200 TEMP(K) = 382.92 PRESS =
> > 0.0
> > Etot = -59487.6114 EKtot = 22560.8324 EPtot =
> > -82048.4438
> > BOND = 16034.9218 ANGLE = 659.4046 DIHED =
> > 390.1891
> > 1-4 NB = 114.1136 1-4 EEL = 42.2749 VDWAALS =
> > 42407.5923
> > EELEC = -142097.1664 EHBOND = 0.0000 RESTRAINT =
> > 400.2265
> > EAMBER (non-restraint) = -82448.6703
> >
> >
> ------------------------------------------------------------------------------
> >
> > NMR restraints: Bond = 400.226 Angle = 0.000 Torsion =
> 0.000
> >
> >
> ===============================================================================
> > vlimit exceeded for step 205; vmax = 10.4966
> > vlimit exceeded for step 209; vmax = 10.8235
> > vlimit exceeded for step 210; vmax = 13.8823
> > vlimit exceeded for step 215; vmax = 10.7677
> > vlimit exceeded for step 228; vmax = 10.5320
> > vlimit exceeded for step 243; vmax = 10.2752
> > vlimit exceeded for step 244; vmax = 10.0241
> > vlimit exceeded for step 250; vmax = 10.5002
> > vlimit exceeded for step 274; vmax = 10.5448
> > vlimit exceeded for step 276; vmax = 10.4640
> > vlimit exceeded for step 290; vmax = 10.0507
> > vlimit exceeded for step 314; vmax = 10.1503
> > vlimit exceeded for step 315; vmax = 10.1877
> >
> > NSTEP = 400 TIME(PS) = 0.400 TEMP(K) = 410.54 PRESS =
> > 0.0
> > Etot = -59146.1463 EKtot = 24188.0949 EPtot =
> > -83334.2413
> > BOND = 18496.4005 ANGLE = 609.2506 DIHED =
> > 419.9729
> > 1-4 NB = 150.6210 1-4 EEL = -5.9135 VDWAALS =
> > 46515.0270
> > EELEC = -150024.2975 EHBOND = 0.0000 RESTRAINT =
> > 504.6977
> > EAMBER (non-restraint) = -83838.9390
> >
> >
> ------------------------------------------------------------------------------
> >
> > Your in site to these files would help me a lot, thank you so much.
> >
> > Best wishes
> >
> > Vince
> >
> > PS: I dont a protocol to perform MD with NMR restraints
> >
> >
> >
> >
> >
> >
> >
> > On 2 November 2015 at 13:38, Carlos Simmerling <
> > carlos.simmerling.gmail.com>
> > wrote:
> >
> > > the vlimit error is not "volume" limit, but velocity. it means there is
> > > probably a mismatch in your input structure and the restraints. I'm not
> > > sure that someone can just provide an input, because it would depend on
> > the
> > > source of your restraints, how they are set up, your input coordinates
> > and
> > > so on. someone may have an automated input for this, but if not and you
> > > want to find out what's going wrong, send more info to the list with
> > > details about how you did the setup and what the first step of
> > minimization
> > > tells you. we'd need to see the energy at step 0 or step 1, no later.
> if
> > > you haven't already carefully looked at this yourself, please do that-
> > > sander gives you a lot of info that can be helpful in understanding
> what
> > is
> > > going on. you are the best person to figure out what that means, since
> > > others probably do not know all of the steps that you already did, and
> > the
> > > details of the molecule you are simulating.
> > >
> > > On Mon, Nov 2, 2015 at 7:29 AM, V. Kumar <vin.vasanth.gmail.com>
> wrote:
> > >
> > > > Dear AMBER users
> > > >
> > > > Could request I request scripts for rMD |or| Distance-Restrained
> > > Molecular
> > > > Dynamics Refinement in Explicit Solvent for AMBER 12 with
> > AMBERTOOL-13. I
> > > > have used one from the internet but it led to volume limit errorr
> with
> > > > vlimit=10, I have changed to vlimti=20, still for few steps it cross
> > like
> > > > 200. So I have tried to perform rMD at in the range 25-30°C still I
> gor
> > > the
> > > > same error. I would highly appreciate if some give me correct
> scripts.
> > > >
> > > > thanks
> > > > Vince
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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(image/png attachment: image.png)
(image/png attachment: paper1.png)
- application/octet-stream attachment: gb_anneal_200ps.in
