# Re: [AMBER] Density for a protein ligand complex run

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Sun, 7 Jun 2015 20:37:59 -0300 (ARGSL-ST)

Dear Jones,

I regret that my comment was seen as sarcastic but I said it as a joke. In
fact one of my coauthors has a garlic on his desktop and I took the idea
from there.
Anyway, as was said, you should check the input geometry carefuly because
the last attached leap.log reports the following paragraph:

(type - hence mass - of one or more atoms could not be found).

This sentence is printed by leap for masses < 0.0. In other words,
somethig wrong is happening with your input file.

My apologies,
Greeting,
Hector.

> 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)
> Reading force field modification type file (frcmod)
> 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.
> 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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>

--------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
I DO NOT DEFINE TIME, SPACE, PLACE, AND MOTION, AS BEING WELL KNOWN TO ALL.
-- NEWTON (1642-1726), PRINCIPIA.

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Received on Sun Jun 07 2015 - 17:00:02 PDT
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