why didn't it work for you? I have used it many times and it works just
fine. perhaps you didn't do proper imaging first?
On Wed, Sep 1, 2010 at 10:41 PM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> For the benefit of others who would read this post in the future, the
> closest command in ptraj is not the suitable program to perform the task of
> filtering closest distance of water O atom to the ligand/protein. Better to
> use VMD for this purpose. Then feed this as input for naccess to get buried
> waters.
>
> Amor
>
> --- On Thu, 19/8/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Cut-off distance "in Closest" command of ptraj
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Thursday, 19 August, 2010, 10:04 PM
>
> I believe for each frame it calculates the distance between the COM of the
> ligand (or center of geometry, not sure which one) and most likely the
> oxygen atom of the water molecule (the COM of the water molecule is not
> much
> different). It compares the distances for all of the water molecules and
> chooses the 10 that have the smallest distance. Note, these are NOT the
> same water molecules in every frame.
>
> Good luck!
> Jason
>
> On Thu, Aug 19, 2010 at 3:14 AM, Amor San Juan <amorsanjuan.yahoo.com
> >wrote:
>
> > Jason, thanks for the reply. To picture out the closest analysis, given
> the
> > example of 50 snapshots in trajectory I issued the closest command to
> search
> > for the 10 closest water near the ligand. The output is P+L+W10
> > (protein+ligand+ten water). My inquiry is how does closest algorithm
> chooses
> > which water are close or far? What is the distance it takes between the
> > ligand and water for the algorithm to differentiate closest and far water
> > molecules. TIP3P water models bounced front and back during the dynamics,
> > and there are water molecules that frequently visit the hydration which
> > could be long/short residency of interaction. In this case, how does
> closest
> > algorithm choose those 10 water closest to the ligand.
> >
> > Amor
> >
> >
> > --- On Wed, 18/8/10, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Cut-off distance "in Closest" command of ptraj
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Wednesday, 18 August, 2010, 9:43 PM
> >
> > There is no cutoff. You provide a number, and it takes that many waters
> > that are closest to the selection. If you choose 10, and the 10th
> closest
> > water is 100 angstroms away, then the cutoff is 100 angstroms. Am I
> > misunderstanding your question?
> >
> > All the best,
> > Jason
> >
> > On Wed, Aug 18, 2010 at 1:35 AM, Amor San Juan <amorsanjuan.yahoo.com
> > >wrote:
> >
> > > What is the cut-off distance between "solute-solvent" implemented in
> > > closest command? It was not specify at the manual. Is it a cut-off
> > distance
> > > of up to 3Angstroms? or perhaps smaller than that, am not sure.
> > >
> > > Thanks Jason for the previous reply, and yes I resolved the problem by
> > > fixing the input script for closest in ptraj. The output trajectory
> > contains
> > > the first 10 closest water, followed by farthest of thousands of tip3p
> > model
> > > water.
> > >
> > > Amor
> > >
> > >
> > >
> > > --- On Tue, 17/8/10, Jason Swails <jason.swails.gmail.com> wrote:
> > >
> > > From: Jason Swails <jason.swails.gmail.com>
> > > Subject: Re: [AMBER] Creating new topology file from close.mdcrd file
> > > To: "AMBER Mailing List" <amber.ambermd.org>
> > > Date: Tuesday, 17 August, 2010, 8:52 PM
> > >
> > > Hello,
> > >
> > > I'm assuming from the next email you sent out that this has been
> > resolved?
> > > I'm also quite certain that the output trajectory written will only
> have
> > > the
> > > 10 appropriate water molecules, not all of them with the first 10
> > > corresponding to the 10 water molecules of interest.
> > >
> > > All the best,
> > > Jason
> > >
> > > On Tue, Aug 17, 2010 at 5:42 AM, Amor San Juan <amorsanjuan.yahoo.com
> > > >wrote:
> > >
> > > > Thanks Jason for always giving time and attention.
> > > >
> > > > The input script I used for closest is:
> > > >
> > > > ----
> > > > trajin CLOin.mdcrd
> > > > trajout CLOout.mdcrd
> > > >
> > > > center :1-200 mass origin
> > > > image origin center
> > > > solvent byres :WAT
> > > > closest 10 :200 first
> > > > -----
> > > >
> > > > The ligand numbering is 200, where I want 10 closest water around it.
> I
> > > got
> > > > the output trajectory but I bumped into another problem of generating
> > the
> > > > new topology file corresponding to "CLOout.mdcrd". This new topology
> > file
> > > > shall be obtained from a new pdb file (P+L+W10) where W10 is 10 water
> > > > molecules. I wanted to do the ff steps:
> > > >
> > > > 1.Take one snapshot from "CLOout.mdcrd" by extraction of trajectory
> > using
> > > > mmpbsa.pl. Convert snapshot to pdb using ambpdb.
> > > > 2. Modify the pdb file such that only 10 water molecules remained,
> > > together
> > > > with prot+lig
> > > > 3.Create new topology using the pdb generated in step2.
> > > >
> > > > File CLOin.mdcrd input trajectory has 37581879 bytes while
> CLOout.mdcrd
> > > > output trajectory has only 4161681 bytes. Input traj contains 9000
> > TIP3P
> > > > model waters, and after executing closest command the output is
> > expected
> > > to
> > > > contain only 10 closest water molecules (but Im not sure of this
> > > > assumption).
> > > >
> > > > My question is: does the output trajectory from "closest" command
> gives
> > > > only the specified number of water? Or, the selected 10 closest water
> > are
> > > > written immediately after prot+lig, and followed by the rest of
> > thousands
> > > of
> > > > tip3p models which are farthest. I need to know precisely so that I
> > will
> > > > track down the error of generating snaphots from CLOout.mdcrd.
> > > >
> > > > In this case, the CLOin.mdcrd has (Prot+Lig+Wat)=PLW.prmtop contains
> > > 30324
> > > > atoms. This PLW.prmtop does not correspond to CLOout.mdcrd, because
> > > whenever
> > > > I tried generating snapshots there is mismatch of atoms. I coudnt be
> > able
> > > to
> > > > generate a pdb file from step1 above.
> > > >
> > > > Mismatch atoms in generating pdb seems to me that PLW10.prmtop should
> > be
> > > > used, but to where I could get it as this is the reason I am doing
> > steps
> > > 1-3
> > > > to get it.
> > > >
> > > > Please anybody help me get from this bump. I have exhausted the
> entire
> > > day.
> > > >
> > > > Amor
> > > >
> > > >
> > > >
> > > > --- On Mon, 16/8/10, Jason Swails <jason.swails.gmail.com> wrote:
> > > >
> > > > From: Jason Swails <jason.swails.gmail.com>
> > > > Subject: Re: [AMBER] How to identify water molecules at the interface
> ?
> > > > follow up ....
> > > > To: "AMBER Mailing List" <amber.ambermd.org>
> > > > Date: Monday, 16 August, 2010, 9:03 PM
> > > >
> > > > Hello,
> > > >
> > > > On Mon, Aug 16, 2010 at 2:19 AM, Amor San Juan <
> amorsanjuan.yahoo.com
> > > > >wrote:
> > > >
> > > > > I want to write a follow-up in regard to my previous post below.
> > > > >
> > > > > Aside from ptraj hbond analysis, I also tried several ptraj
> commands
> > > > > including:
> > > > > a) grid = the aim of this command is to generate water density at
> > > > hydration
> > > > > b)watershell= the aim of this command is to count the number of
> water
> > > > > molecules at 1st/2nd solvation shell
> > > > > c) closest= the aim of this command is to quantify the number of
> > water
> > > > > molecules at 3.5A and 5A.
> > > > >
> > > > > In all those commands above, I am unable to identify the numbering
> of
> > > > water
> > > > > buried at interface. Although the closest command can quantify the
> > > water
> > > > > molecules at specific distance, its numbering of water molecules
> were
> > > > > altered compared to the original numbering.
> > > > >
> > > > > My aim is to get the identity of the water molecules buried between
> > the
> > > > > ligand-protein. Once the water identity is found, I will use this
> as
> > > > input
> > > > > together with prot+lig for binding energy calculation in mmpbsa.
> What
> > I
> > > > mean
> > > > > to say in water identity is simply the water identity as reflected
> on
> > > its
> > > > > atom/residue number.
> > > > >
> > > >
> > > > You don't need this really. Just create a new prmtop and trajectory
> > file
> > > > with only the proper number of waters that you kept with the
> "closest"
> > > > command. Then it doesn't matter what the original numbering was in
> the
> > > > prmtop/trajectory file(s), it's simply the new numbers it has in the
> > new
> > > > trajectory. Then feed this into MMPBSA and don't tell it to strip
> any
> > > > waters/ions. For example, if you're using MMPBSA.py, set
> strip_mdcrd=0
> > > to
> > > > avoid stripping the trajectory file of any waters/ions. For
> > mm_pbsa.pl,
> > > > just include the water atoms as part of the ligand or receptor atoms.
> > > >
> > > > Hope this helps,
> > > > Jason
> > > >
> > > >
> > > > > amor
> > > > >
> > > > >
> > > > > --- On Mon, 16/8/10, Amor San Juan <amorsanjuan.yahoo.com> wrote:
> > > > >
> > > > > From: Amor San Juan <amorsanjuan.yahoo.com>
> > > > > Subject: How to identify water molecules at the interface ?
> > > > > To: "AMBER Mailing List" <amber.ambermd.org>
> > > > > Date: Monday, 16 August, 2010, 11:51 AM
> > > > >
> > > > > I have read several posts regarding water calculations in several
> > ways
> > > > for
> > > > > different purposes done. But it seems to me that the goal I want to
> > > > achieve
> > > > > needs relevant feedback from the forum.
> > > > >
> > > > > I have a system (protein + peptide + ligand) with 200 residues in
> > total
> > > > and
> > > > > note that ligand has a phosphate group. I want to identify the
> water
> > > > > molecules (TIP3P models) found at the interface between the ligand
> > and
> > > > > protein. I need to identify which water molecules are at the
> > interface
> > > so
> > > > I
> > > > > can use it as input for binding energy calculation by MMPBSA. Here
> > are
> > > > the
> > > > > steps formulated for water identification:
> > > > >
> > > > > 1) Calculate the water within 3.5Angstroms using the trajectory
> > input.
> > > > The
> > > > > expected outcome is (P+L+Wi) such that P=protein, L=ligand, and
> > > Wi=water
> > > > at
> > > > > ith frame. From the output, remove all hydrogen molecules in water.
> > > > >
> > > > > 2)Calculate accessibility by
> > > > > filtering out WAT.O (Water oxygen) within >0.50Angstroms
> > > > >
> > > > > 3) Repeat step 2 to get only the buried water molecules remaining
> at
> > > > > interface.
> > > > >
> > > > > One suggestion I got is to make a script to do in one shot the
> above
> > > > three
> > > > > steps. I think about it but am not sure if one straightforward
> script
> > > can
> > > > do
> > > > > the task.
> > > > >
> > > > > I approached the problem by trying to do it one-step-at-a-time. For
> > > step
> > > > 1
> > > > > above, I implemented ptraj. Using ptraj h-bond distance 3.5
> analysis,
> > > it
> > > > > gave me an output of P+L+Wi, however looking at Wi seems to be so
> > > > enormous
> > > > > from the list as expected.
> > > > > For step2, I need the trajectory that contains P+L+Wi with stripped
> > > > > hydrogens generated from step1. I have not proceeded to step2 yet.
> > > > >
> > > > > To get the trajectory P+L+Wi, it seems the way out is to use the
> > > > > ptraj-hbond output to select interacting atoms, but as noted Wi in
> > the
> > > > list
> > > > > is quite long to do manual selection one-by-one.
> > > > >
> > > > > I also thought of using LIGPLOT program to
> > > > > identify buried water molecules but my input is a trajectory not a
> > > pdb.
> > > > I
> > > > > know I can generate pdb from snapshots in trajectory but how would
> > you
> > > > take
> > > > > it for several thousands of snapshots pdb? Bottomline, I only need
> to
> > > > > identify the water at interface based on the trajectory.
> > > > >
> > > > > Amor
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 02 2010 - 04:30:05 PDT
