Hi Hector,
I did the simulation again using the forcefield ff14SB as suggested and
using the scripts sent by you.
leap.log looks like this:
Adding box at: x=7 y=7 z=4
Center of solvent box is: -65.710222, -65.710222, -9.387175
Adding box at: x=7 y=7 z=5
Center of solvent box is: -65.710222, -65.710222, -28.161524
Adding box at: x=7 y=7 z=6
Center of solvent box is: -65.710222, -65.710222, -46.935873
Adding box at: x=7 y=7 z=7
Center of solvent box is: -65.710222, -65.710222, -65.710222
(using default radius 1.500000 for Cl-)
(using default radius 1.500000 for Cl-)
(using default radius 1.500000 for Cl-)
(using default radius 1.500000 for Cl-)
(using default radius 1.500000 for Cl-)
(using default radius 1.500000 for Cl-)
Volume: 1176727.919 A^3 (oct)
Mass > 652639.550 amu, Density > 0.921 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 34845 residues.
>loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /opt/apps/amber14/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
> saveamberparm k file.top file.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: 0.998000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
1-4: angle 3452 3459 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3446 3454 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3438 3439 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 3437 3440 duplicates bond ('triangular' bond) or angle ('square'
bond)
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for n-h2-cy-ss
atoms are: N4 H C5 S3
** Warning: No sp2 improper torsion term for n-h2-cy-cy
atoms are: N4 H C5 C6
** Warning: No sp2 improper torsion term for n-ss-cy-cy
atoms are: N4 S3 C5 C6
** Warning: No sp2 improper torsion term for h2-ss-cy-cy
atoms are: H S3 C5 C6
** Warning: No sp2 improper torsion term for n-os-cy-c
atoms are: N5 O4 C6 C7
** Warning: No sp2 improper torsion term for n-os-cy-cy
atoms are: N5 O4 C6 C5
** Warning: No sp2 improper torsion term for n-c-cy-cy
atoms are: N5 C7 C6 C5
** Warning: No sp2 improper torsion term for os-c-cy-cy
atoms are: O4 C7 C6 C5
** Warning: No sp2 improper torsion term for ss-h2-cy-c
atoms are: S2 H7 C9 C8
** Warning: No sp2 improper torsion term for ss-h2-cy-ss
** Warning: No sp2 improper torsion term for ss-h2-cy-ss
atoms are: S2 H7 C9 S1
** Warning: No sp2 improper torsion term for ss-c-cy-ss
atoms are: S2 C8 C9 S1
** Warning: No sp2 improper torsion term for h2-c-cy-ss
atoms are: H7 C8 C9 S1
old PREP-specified impropers:
<DRG 213>: C11 N6 C12 O2
<DRG 213>: C12 H8 N6 H9
<DRG 213>: C12 C13 C11 C10
<DRG 213>: C11 O3 C13 O6
<DRG 213>: C11 S1 C10 S2
<DRG 213>: C9 N5 C8 O1
<DRG 213>: C8 C6 N5 H6
<DRG 213>: C6 N4 C7 O
<DRG 213>: C7 C4 N4 C5
<DRG 213>: C3 C16 C4 N4
<DRG 213>: C4 O5 C16 O7
<DRG 213>: C15 C2 C3 C4
<DRG 213>: N N1 C1 S
<DRG 213>: C C1 N N3
total 711 improper torsions applied
14 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CCYS 1
NMET 1
WAT 34845
)
(no restraints)
> quit
And the summary.DENSITY looks like:
55.000 0.9855
60.000 0.9917
65.000 0.9928
70.000 0.9928
75.000 0.9935
80.000 0.9933
85.000 0.9944
90.000 0.9939
95.000 0.9937
100.000 0.9926
105.000 0.9934
110.000 0.9950
115.000 0.9927
120.000 0.9936
The out file has been run for till now...
NSTEP = 5000000 TIME(PS) = 30050.000 TEMP(K) = 299.99 PRESS =
4.2
Etot = -206659.9413 EKtot = 49032.6650 EPtot =
-255692.6063
BOND = 697.6952 ANGLE = 1842.6901 DIHED =
2385.6542
1-4 NB = 784.6829 1-4 EEL = 4981.9735 VDWAALS =
34935.9089
EELEC = -301321.2111 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 23307.9527 VIRIAL = 23234.0444 VOLUME =
820161.0029
Density =
0.9979
RMS calculation script
trajin npt_MS.mdcrd
trajin npt_MS2.mdcrd
trajin npt_MS3.mdcrd
autoimage
trajout npt_MS_all3reimg.mdcrd
rms first out rms.out .CA,C,N, time 10.0
The rmsd for the same shows stablising around 11 Angstrom
59610.000 10.9905
59620.000 11.1655
59630.000 11.1025
59640.000 11.0785
59650.000 11.1712
59660.000 11.2284
59670.000 11.3872
59680.000 11.4965
59690.000 11.5443
59700.000 11.3725
59710.000 11.3509
59720.000 11.2027
59730.000 11.2712
59740.000 11.2898
59750.000 11.2370
59760.000 11.1258
59770.000 11.1687
59780.000 11.1122
59790.000 11.0479
59800.000 11.2534
59810.000 11.1920
59820.000 11.2822
59830.000 11.2291
59840.000 11.1727
59850.000 11.1325
59860.000 11.2933
59870.000 11.2510
59880.000 11.2540
59890.000 11.3308
59900.000 11.3084
59910.000 11.2239
59920.000 11.3312
59930.000 11.3771
59940.000 11.3447
59950.000 11.4072
59960.000 11.3195
59970.000 11.3988
59980.000 11.4998
59990.000 11.4432
60000.000 11.4997
What can we infer now from the results?
Also the density still remains less than 1 gm/cc any suggestions why?
Thank you.
M.Jones
On Wed, Jun 3, 2015 at 6:44 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Wed, Jun 03, 2015, Mrinda Jones wrote:
> >
> > The system details are:
> > Force field : gaff and ff99SB
> > System Length : 212 residues (protein) and one Drug
> > Overall Protein is Neutral and Drug has -2 Net charge
> > Thermostat and barostat used: Langevin thermostat (NTT=3),
> > MC Barostat was default i.e 1, ntp=1
> >
> >
> > My question is, is this density being less than 1gg/cc justifiable in
> terms
> > of MD run. Is the run okay?
>
> Based on what you report, I would not view a density of 0.98 as a red flag.
>
> > What can a rmsd data tell about the simulation? Is it necessary for the
> > rmsd to get stabilized below 3 or 4 Angstrom in case of modeled protein
> > runs as well as there is an non-modeled loop region towards the
> > protein-tail.
>
> It is not clear what reference structure you are using for the RMSD
> calculation.
>
> In cases like this, it is often very helpful to compute the backbone RMSD
> leaving out loops and tails. But there is no magic number: visually
> comparing
> the starting and ending structures will tell you whether the overall fold
> has
> changed or not. In a 200 residue protein, you can easily get RMSD values
> of 3
> or 4 Ang (espeically if you are including loops and tails) when the overall
> fold has changed very little.
>
> ...dac
>
>
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>
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Received on Fri Jun 05 2015 - 11:30:03 PDT
