In absolute binding free energies, your endpoints are:
Ligand (fully charge, fully interacting), ligand (no charge full interacting), nothing (no charge not interacting)
Decharge does (fully charge, fully interacting) -> (no charge, fully interacting)
VDW does (no charge, fully interacting) -> (no charge, not interacting)
Therefore you don't need a recharge step.
Essentially timask1 and timask2 define your endpoints of your lambda windows (0.0 and 1.0).
On 10/14/19, 11:11 AM, "Sadaf Rani" <sadafrani6.gmail.com> wrote:
CAUTION: EXTERNAL EMAIL
Dear Amber and Charles
In this case, do I need to run a recharge state also?
Could you please brief a bit more, As I am trying this for the first time I
have confusion about setting up the system that when I am using vdw
interactions does it contains parameters of both states? and for decharge I
need to strip the first state?
I need your suggestions, please.
Thank you
Sadaf
On Mon, Oct 14, 2019 at 3:20 PM Charles Lin <Charles.lin.silicontx.com>
wrote:
> You shouldn't use softcore if your coordinates are being scaled together
> (turn off both your scmasks). Yea the chargemask literally just sets the
> charge of the atoms you indicate to 0, so you could have done it through
> the parameterization or through the crgmask flag, so that's working as
> intended.
>
> On 10/14/19, 6:59 AM, "Sadaf Rani" <sadafrani6.gmail.com> wrote:
>
>
> CAUTION: EXTERNAL EMAIL
>
>
>
> Dear Charles
> I set my system in which BG0 library contains charges however there is
> no
> charge for BG1 state and I combined the two with same coordinates and
> parameters in the same file after that I run a short minimization with
> inputs as below:-
>
> minimization
>
> &cntrl
>
> imin = 1, ntmin = 2,
>
> maxcyc = 100,
>
> ntpr = 20, ntwe = 20,
>
> ntb = 1,
>
> ntr = 1, restraint_wt = 5.00,
>
> restraintmask='!:WAT & !.H=',
>
>
>
> icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5, scbeta = 12.0,
>
> logdvdl = 0,
>
> timask1 = ':BG0', timask2 = ':BG1',
>
> scmask1 = ':BG0', scmask2 = ':BG1'
>
> crgmask=':BG1'
>
> /
>
> &ewald
>
> /
>
>
>
> It gives me following in output calculation:-
>
> 5. REFERENCE ATOM COORDINATES
>
> default_name
>
> Mask !:WAT & !.H=; matches 32 atoms
> TI Mask 1 :BG0; matches 27 atoms
> TI Mask 2 :BG1; matches 27 atoms
> TI region 1: 8682 atoms
> TI region 2: 8682 atoms
> SC Mask 1 :BG0; matches 27 atoms
> SC Mask 2 :BG1; matches 27 atoms
> Removing charge of 0.0000 from atom 28
> Removing charge of 0.0000 from atom 29
> Removing charge of 0.0000 from atom 30
> Removing charge of 0.0000 from atom 31
> Removing charge of 0.0000 from atom 32
> Removing charge of 0.0000 from atom 33
> Removing charge of 0.0000 from atom 34
> Removing charge of 0.0000 from atom 35
> Removing charge of 0.0000 from atom 36
> Removing charge of 0.0000 from atom 37
> Removing charge of 0.0000 from atom 38
> Removing charge of 0.0000 from atom 39
> Removing charge of 0.0000 from atom 40
> Removing charge of 0.0000 from atom 41
> Removing charge of 0.0000 from atom 42
> Removing charge of 0.0000 from atom 43
> Removing charge of 0.0000 from atom 44
> Removing charge of 0.0000 from atom 45
> Removing charge of 0.0000 from atom 46
> Removing charge of 0.0000 from atom 47
> Removing charge of 0.0000 from atom 48
> Removing charge of 0.0000 from atom 49
> Removing charge of 0.0000 from atom 50
> Removing charge of 0.0000 from atom 51
> Removing charge of 0.0000 from atom 52
> Removing charge of 0.0000 from atom 53
> Removing charge of 0.0000 from atom 54
> Total charge of 0.00000000 removed from 27 atoms
>
>
> Am I doing right? crgmask=':BG1' indicates that charges are already
> removed from the BG1 state then why I am getting this charge removal
> data
> is regarding BG1?
> I have attached the output file for reference.
> I need your guideline, please.
> thank you in advance.
>
> Sadaf
>
>
> On Thu, Oct 10, 2019 at 7:51 PM Charles Lin <Charles.lin.silicontx.com
> >
> wrote:
>
> > Yea you basically want an identical copy of the ligand (same
> parameters,
> > same coordinates). You can use the combine call in tleap to create a
> > topology this way (similar to how you use the combine call in a
> relative
> > binding free energy calculation.
> >
> > On 10/10/19, 10:45 AM, "Sadaf Rani" <sadafrani6.gmail.com> wrote:
> >
> >
> > CAUTION: EXTERNAL EMAIL
> >
> >
> >
> > Dear Charles
> > thank you for your reply
> > I am a bit confused here. For system set up do I need to build a
> second
> > copy of ligand (BG7) mentioned above which has no charge on it
> and
> > save the
> > coordinates of both states (BG6 & BG7) in the same prmtop file?
> > Could you please elaborate a little more regarding the setting
> up of
> > system?
> > Also for vdw state, should I set my system like this?
> >
> > icfe = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
> > logdvdl = 1,
> >
> > ifmbar = 1, mbar_states= 11,
> >
> > mbar_lambda= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,
> 0.9, 1.0
> >
> > bar_intervall = 10,
> >
> > timask1 = ':BG6', timask2 = '',
> >
> > ifsc = 1, crgmask = ':BG7',
> > scmask1=':BG6' scmask2='BG7'
> > crgmask=':BG6'
> >
> > looking forward to hear from you soon.
> >
> > Thank you
> >
> > Sadaf
> >
> >
> > On Thu, Oct 10, 2019 at 2:13 PM Charles Lin <
> Charles.lin.silicontx.com
> > >
> > wrote:
> >
> > > For decharge step you generally want your endstates to be:
> > > Lambda 0: Molecule with charge
> > > Lambda 1.0: Molecule without charge
> > >
> > > Therefore you'd want 2 copies of your ligand.
> > >
> > > So you'd want
> > > Timask1=':BG6', timask2=':BG7' (or whatever second copy of your
> > ligand is)
> > > crgmask=':BG7'
> > >
> > > On 10/10/19, 8:16 AM, "Sadaf Rani" <sadafrani6.gmail.com>
> wrote:
> > >
> > >
> > > CAUTION: EXTERNAL EMAIL
> > >
> > >
> > >
> > > Dear Amber and Charlie
> > > I run TI calculation for calculating absolute free energy
> > calculation
> > > of
> > > ligand with the following input in decharge step:-
> > >
> > > icfe = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
> > > logdvdl = 1,
> > >
> > > ifmbar = 1, mbar_states= 11,
> > >
> > > mbar_lambda= 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,
> 0.8,
> > 0.9, 1.0
> > >
> > > bar_intervall = 10,
> > >
> > > timask1 = ':BG6', timask2 = '',
> > >
> > > ifsc = 0, crgmask = ':BG6',
> > >
> > > but it gives me following error:-
> > >
> > > TI Mask 1 :BG6; matches 27 atoms
> > > TI Mask 2 matches 0 atoms
> > > TI region 1: 8591 atoms
> > > TI region 2: 8564 atoms
> > > Removing charge of -0.6555 from atom 1
> > > Removing charge of 0.4043 from atom 2
> > > Removing charge of 0.1047 from atom 3
> > > Removing charge of 0.0443 from atom 4
> > > Removing charge of 0.2450 from atom 5
> > > Removing charge of -0.7348 from atom 6
> > > Removing charge of 0.4283 from atom 7
> > > Removing charge of -0.0045 from atom 8
> > > Removing charge of 0.2380 from atom 9
> > > Removing charge of -0.7107 from atom 10
> > > Removing charge of 0.4056 from atom 11
> > > Removing charge of 0.0704 from atom 12
> > > Removing charge of 0.5188 from atom 13
> > > Removing charge of -0.7055 from atom 14
> > > Removing charge of 0.4528 from atom 15
> > > Removing charge of -0.0204 from atom 16
> > > Removing charge of -0.5253 from atom 17
> > > Removing charge of 0.2104 from atom 18
> > > Removing charge of 0.0424 from atom 19
> > > Removing charge of 0.2913 from atom 20
> > > Removing charge of -0.0024 from atom 21
> > > Removing charge of -0.0024 from atom 22
> > > Removing charge of -0.5859 from atom 23
> > > Removing charge of 1.3045 from atom 24
> > > Removing charge of -0.9377 from atom 25
> > > Removing charge of -0.9377 from atom 26
> > > Removing charge of -0.9377 from atom 27
> > > Total charge of -2.00000000 removed from 27 atoms
> > >
> > > MBAR - lambda values considered:
> > > 11 total: 0.0000 0.1000 0.2000 0.3000 0.4000 0.5000
> 0.6000
> > > 0.7000
> > > 0.8000 0.9000 1.0000
> > > Extra energies will be computed 10000 times.
> > > Checking for mismatched coordinates.
> > > ERROR: timask1/2 must match the same number of atoms
> for
> > > non-softcore
> > > run
> > >
> > > how should I set input to fix this error
> > > Looking forward to hearing from you.
> > > thank you
> > >
> > > Sadaf
> > >
> > > On Thu, Oct 3, 2019 at 5:13 PM Charles Lin <
> > Charles.lin.silicontx.com>
> > > wrote:
> > >
> > > > You essentially just need to run your production scheme
> with
> > > different
> > > > lambdas by changing the clambda value.
> > > >
> > > > 0.0 = your ligand fully exists
> > > > 1.0 = your ligand has fully disappeared.
> > > >
> > > > Follow the folder setup like this:
> > > >
> http://ambermd.org/tutorials/advanced/tutorial9/index.html
> > > >
> > > > You may want to increase the number of lambda windows
> you're
> > using
> > > because
> > > > your transformation is a lot bigger when you're
> augmenting both
> > > > electrostatics and vdws. You may want to considering
> doing it
> > in
> > > two steps
> > > > where you first decharge your molecule then disappear
> the vdws.
> > > (Similar
> > > > to the tutorial except scmask2 and timask2 are both '',
> and you
> > > don't run a
> > > > recharge window.
> > > >
> > > > -Charlie
> > > >
> > > > On 10/3/19, 11:06 AM, "Sadaf Rani" <sadafrani6.gmail.com
> >
> > wrote:
> > > >
> > > >
> > > > CAUTION: EXTERNAL EMAIL
> > > >
> > > >
> > > >
> > > > Dear Amber
> > > > I am also looking for the same.
> > > > I have a ligand for my protein for which I want to
> > calculate
> > > absolute
> > > > binding energy; in which I want the ligand to
> disappear
> > > completely at
> > > > the
> > > > start and then appear with all vander waals and
> > electrostatic
> > > > interactions.
> > > > As per my understanding(I may be wrong in it), I
> should
> > set up
> > > my
> > > > ligand
> > > > in solution and complex in solution as per the
> following
> > input:-
> > > > Minimization:-
> > > > &cntrl
> > > > imin = 1, ntmin = 2,
> > > > maxcyc = 1000,
> > > > ntpr = 200, ntwe = 200,
> > > > ntb = 1,
> > > > ntr = 1, restraint_wt = 5.00,
> > > > restraintmask='!:WAT & !.H=',
> > > >
> > > > icfe = 1, ifsc = 1, clambda = 0.0, scalpha = 0.5,
> > scbeta =
> > > 12.0,
> > > > logdvdl = 0,
> > > > timask1=':1', scmask1=':1',
> > > > timask2='', scmask2='',
> > > > /
> > > > &ewald
> > > > /
> > > >
> > > > Heating:-
> > > > &cntrl
> > > > imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt =
> > 0.002,
> > > > nmropt = 1,
> > > > ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
> > > > ntb = 1,
> > > > ntc = 2, ntf = 1,
> > > > ioutfm = 1, iwrap = 1,
> > > > ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr =
> 5000,
> > > >
> > > > ntr = 1, restraint_wt = 5.00,
> > > > restraintmask='!:WAT & !.H=',
> > > >
> > > > icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5,
> > scbeta =
> > > 12.0,
> > > > logdvdl = 0,
> > > > timask1=':1', scmask1=':1',
> > > > timask2='', scmask2='',
> > > > /
> > > > &ewald
> > > > /
> > > >
> > > > &wt
> > > > type='TEMP0',
> > > > istep1 = 0, istep2 = 8000,
> > > > value1 = 5.0, value2 = 300.0
> > > > /
> > > >
> > > > &wt type = 'END'
> > > > /
> > > >
> > > > Pressurizing:-
> > > > &cntrl
> > > > imin = 0, nstlim = 10000, irest = 1, ntx = 5, dt =
> > 0.002,
> > > > ntt = 1, temp0 = 300.0, tautp = 1.0,
> > > > ntp = 1, pres0 = 1.0, taup = 2.0,
> > > > ntb = 2,
> > > > ntc = 2, ntf = 1,
> > > > ioutfm = 1, iwrap = 1,
> > > > ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr =
> 5000,
> > > >
> > > > ntr = 1, restraint_wt = 5.00,
> > > > restraintmask='!:WAT & !.H=',
> > > >
> > > > icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5,
> > scbeta =
> > > 12.0,
> > > > logdvdl = 0,
> > > > timask1=':1', scmask1=':1',
> > > > timask2='', scmask2='',
> > > > /
> > > > &ewald
> > > > /
> > > > What next? How to set input for absolute free energy
> > > calculations in
> > > > order
> > > > to disappear ligand and slowly appear with increase
> in
> > lambda?
> > > >
> > > > Looking for your kind suggestions, please.
> > > >
> > > > Thank you
> > > >
> > > >
> > > > On Wed, Oct 2, 2019 at 4:20 PM Charles Lin <
> > > Charles.lin.silicontx.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I'd follow mostly the same protocol as a relative
> > binding free
> > > energy
> > > > > (where ligand a transforms to ligand b), but
> instead of
> > having
> > > a
> > > > ligand b,
> > > > > your timask, scmask of those regions becomes
> nothing
> > > > > timask2='', scmask2='',
> > > > >
> > > > > I would also apply the virtual bond algorithm
> described
> > here
> > > to keep
> > > > your
> > > > > ligand in the pocket (described as a virtual bond
> here)
> > > > > https://pubs.acs.org/doi/pdf/10.1021/jp505777n
> > > > >
> > > > > These calculations are fairly expensive to
> calculate.
> > Relative
> > > > binding
> > > > > free energies converge a lot more quickly because
> the
> > amount of
> > > > phase space
> > > > > to sample is already somewhat more limited due to
> the
> > presence
> > > of a
> > > > ligand
> > > > > you already know its binding pose/pocket
> position. The
> > less
> > > data
> > > > you know
> > > > > about your system, the less likely you'll place
> your
> > ligand
> > > > correctly, and
> > > > > simple changes such as having a side chain
> incorrect,
> > could
> > > vastly
> > > > give
> > > > > different absolute binding free energy values.
> > > > >
> > > > > -Charlie
> > > > >
> > > > > On 10/1/19, 4:26 PM, "Debarati DasGupta" <
> > > > debarati_dasgupta.hotmail.com>
> > > > > wrote:
> > > > >
> > > > >
> > > > > CAUTION: EXTERNAL EMAIL
> > > > >
> > > > >
> > > > >
> > > > > Dear All,
> > > > >
> > > > > I have been trying to read more about free
> energy
> > > calculations
> > > > using
> > > > > TI method implemented in AMBER18. I recently did a
> > webinar by
> > > CCG
> > > > group
> > > > > wherein in MOE2019 they have incorporated the TI
> > > implementation setup
> > > > > collaborating with AMBER.
> > > > >
> > > > > I did read this publication too from Professor
> Carlos
> > > > Simmerling’s
> > > > > webpage “
> > > > >
> > > >
> > >
> >
> https://chemrxiv.org/articles/Blinded_Prediction_of_Protein-Ligand_Binding_Affinity_Using_Amber_Thermodynamic_Integration_for_the_2018_D3R_Grand_Challenge_4/8312375/1
> > > > > ”
> > > > > This did throw a lot of light on how to
> exactly
> > setup TI
> > > > calculations
> > > > > in AMBER.
> > > > >
> > > > > I still have a very fundamental question, it
> may be
> > very
> > > stupid,
> > > > but I
> > > > > am not sure how to setup TI to calculate the
> absolute
> > binding
> > > > affinity of a
> > > > > ligand towards a protein.
> > > > > Is there something I am missing totally?
> > > > > My protein of interest is ABL-kinase and I
> have a
> > done some
> > > > co-solvent
> > > > > simulations to get some hotspots( areas of possible
> > > ligandibility);
> > > > I need
> > > > > to calculate the binding affinity of these small
> > cosolvents
> > > towards
> > > > ABL.
> > > > > TI methods give us a “deldelG”, which is
> relative
> > binding
> > > > affinity, if
> > > > > we have a receptor (say CathepsinS) and have a set
> of 10+
> > > ligands
> > > > with a
> > > > > common core (scaffold).
> > > > > If I have one protein +1 ligand and I need to
> > calculate the
> > > > binding
> > > > > affinity what is the procedure to be adopted?
> > > > > Is there a tutorial to do that?
> > > > >
> > > > > I am not looking to do MMGBSA/PBSA on this
> system.
> > > > >
> > > > > Thanks
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > >
> http://lists.ambermd.org/mailman/listinfo/amber
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> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> This email message is for the sole use of the intended recipient(s)
> and may contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not the
> intended recipient, please contact the sender by reply email and destroy
> all copies of the original message. If you are the intended recipient,
> please be advised that the content of this message is subject to access,
> review and disclosure by the sender's Email System Administrator.
>
>
> This email message is for the sole use of the intended recipient(s) and
> may contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not the
> intended recipient, please contact the sender by reply email and destroy
> all copies of the original message. If you are the intended recipient,
> please be advised that the content of this message is subject to access,
> review and disclosure by the sender's Email System Administrator.
> _______________________________________________
> 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
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 14 2019 - 10:00:02 PDT
