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. 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.
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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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- application/octet-stream attachment: anneal.in
Received on Mon Nov 02 2015 - 07:30:03 PST
