I used ff14SB for protein and glycam forcefield for glycans
________________________________
From: Jason Swails <jason.swails.gmail.com>
Sent: Monday, July 24, 2017 5:21:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters
What force field did you use?
On Thu, Jul 13, 2017 at 6:58 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
wrote:
>
> Hi,
>
> I've now loaded the prmtop into parmed and used printLJTypes to get an
> output of the atom types in the 23 LJ Index types.
> I then manually inspected each Index type in the list to see if some atoms
> within a particular index type have differing LJ parameters
>
> eg. printDetails .%C,C0,CA,C*,CW
>
> Atoms in each of these indices have identical LJ parameters. I could not
> detect a second set of parameters for any of the atom types.
>
> Here is the output:
>
> LJ Type IndexAtom type LJ radiusLJ depth
> 1 N3, N, Ng, X2, X11.82400.1700
> 2 H 0.60000.0157
> 3 CX, 2C, 3C, CT, Cg1.90800.1094
> 4 HP 1.10000.0157
> 5 HC 1.48700.0157
> 6 C, C0, CA, C*, CW1.90800.0860
> 7 O, O2 1.66120.2100
> 8 H1 1.38700.0157
> 9 HA 1.45900.0150
> 10 Oh, OH 1.72100.2104
> 11 HO 0.00000.0000
> 12 H4 1.40900.0150
> 13 H5 1.35900.0150
> 14 S 2.00000.2500
> 15 H2 1.28700.0157
> 16 Os, Oy 1.68370.1700
> 17 Ho 0.20000.0300
> 18 Z1 (ZN) 1.39500.0149
> 19 Cl- 2.25200.6029
> 20 X4 (WT1 O) 1.76830.1520
> 21 HW (WT1 TIP3P H)0.00000.0000
> 22 Na+ 1.47500.0317
> 23 OW (TIP3P O) 1.76830.1520
>
> Could this perhaps mean that I don't have to worry about this warning and
> that the downstream programs will all work properly?
> Or is there another way in which I can try to find the source of error?
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
> ________________________________________
> From: Lizelle Lubbe
> Sent: 13 July 2017 11:03 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters
>
> Hi Daniel,
>
> Thanks for the helpful reply - it makes more sense now.
> I've had a look at the prmtop manual describing the different flags but I
> am still stuck.
> If I haven't modified any LJ parameters willingly (and therefore don't
> know the atom type for which there are more than 1 set of LJ parameters),
> how would I be able to fix this?
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
> ________________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: 12 July 2017 03:30:05 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters
>
> Hi,
>
> "Modified off-diagonal LJ parameters" means an atom type has more than
> one set of LJ parameters associated with it. Normally each atom type
> has one set of LJ parameters (energy well depth and sigma) which are
> combined with the parameters from another type in order to obtain the
> A and B parameters used in the common form of the 6-12 potential term.
> So given 3 atom types A, B, and C you have:
>
> AA
> AB
> AC
> BB
> BC
> CC
>
> It's simple to envision this as a symmetric half matrix (although
> harder to display with a non-fixed-width font):
>
> AA
> AB BB
> AC BC CC
>
> If you know the combining rules used, you can back-calculate the
> original LJ params from the self (diagonal) terms.
>
> One school of thought is that in some cases, these LJ parameters need
> to be adjusted between different atom types; essentially saying
> something like "A" should look different to "B" than it does to "C".
> So you might have 'A' parameters for 'AA' and 'AC', but 'a' parameters
> for 'B':
>
> AA
> aB BB
> AC BC CC
>
> The 'aB' term is a modified off-diagonal LJ term.
>
> TL;DR: I'm not sure how MCPB.py assigns parameters, but it's possible
> that it does create some off-diagonal LJ modifications. Hopefully an
> MCPB.py developer can comment on this.
>
> -Dan
>
> On Wed, Jul 12, 2017 at 8:23 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
> wrote:
> > Hi all,
> >
> > I have searched online for a solution to this problem but found nothing
> yet. Any suggestions??
> >
> > I've done some digging and saw that the frcmod file generated by MCPB.py
> gives the following Lennard Jones parameters (X1-X4 are the 4 coordinating
> ligands and Z1 the zinc ion)
> >
> > NONB
> > X1 1.8240 0.1700 OPLS
> > X2 1.8240 0.1700 OPLS
> > X3 1.6612 0.2100 OPLS
> > X4 1.7683 0.1520 TIP3P water model
> > Z1 1.395 0.0149170000 IOD set from Li et al. JCTC,
> 2013, 9, 2733
> >
> > This is identical to that given in the tutorial example's frcmod file.
> >
> > Using parmed to check the zinc ion in my prmtop gives:
> > ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass
> Charge GB Radius GB Screen
> > 9749 613 ZN1 ZN Z1 1.3950 0.0149 65.4000
> 1.4993 1.5000 0.8000
> >
> >> printLJTypes .ZN
> >
> > ATOM NUMBER NAME TYPE
> > ---------------------------------------------
> > ATOM 9749 ZN Z1 : Type index: 15
> >
> >> checkValidity
> > Determining validity of prmtop
> > 1 total warnings
> >
> > NonUniversalWarning: Modified off-diagonal LJ parameters detected
> >
> > The tutorial's prmtop gives essentially the same (except for charge)
> > ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass
> Charge GB Radius GB Screen
> > 4018 256 ZN1 ZN M1 1.3950 0.0149
> 65.4000 0.4335 1.5000 0.8000
> >
> >> printLJTypes .ZN
> >
> > ATOM NUMBER NAME TYPE
> > ---------------------------------------------
> > ATOM 4018 ZN M1 : Type index: 15
> >
> >> checkValidity
> > Determining validity of prmtop
> > 1OKL_solv.prmtop looks OK to me!
> >
> > This time there is no warning message so I guess it has nothing to do
> with using newly derived parameters as I previously thought.
> > Given that I never changed any LJ parameters in parmed, shouldn't the
> matrix be correctly written from the forcefield information?
> >
> > Does anyone have a suggestion as to the source of this warning and how
> to solve it?
> >
> > Kind regards
> >
> > Lizelle Lubbe
> >
> > PhD (Medical biochemistry) candidate
> > Department of Integrative Biomedical Sciences
> > University of Cape Town
> > ________________________________________
> > From: Lizelle Lubbe
> > Sent: 11 July 2017 05:00:59 PM
> > To: amber.ambermd.org
> > Subject: parmed validity off-diagonal LJ parameters
> >
> > Dear Amber users,
> >
> > I want to simulate a zinc metalloprotease and have determined the metal
> site parameters using MCPB.py
> > After tleap I ran the prmtop through cpptraj and got the following error:
> >
> > Error: Atom 12495 was assigned a lower molecule # than previous atom.
> This can
> > Error: happen if 1) bond information is incorrect or missing, or 2) if
> the
> > Error: atom numbering in molecules is not sequential. If topology did
> not
> > Error: originally contain bond info, 1) can potentially be fixed by
> > Error: increasing the bondsearch cutoff offset (currently 0.200). 2)
> can be
> > Error: fixed by either using the 'fixatomorder' command, or using
> > Error: the 'setMolecules' command in parmed.py.
> > Error: Could not determine molecule information for
> editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop.
> > Error: SetSolventInfo: No molecule information.
> > Error: Could not determine solvent information for
> editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop.
> >
> > Using setMolecules in parmed.py gave a new prmtop with no errors in
> cpptraj.
> >
> > Running parmed and checkValidity on the new prmtop gave the following
> warning:
> >> checkValidity
> > Determining validity of prmtop
> > 1 total warnings
> > NonUniversalWarning: Modified off-diagonal LJ parameters detected
> >
> > I have not changed the LJ parameters in parmed.
> >
> > Jason Swails mentioned in a previous post (Curious behavior of cpptraj
> in ambertools 13.1):
> >> Hmm... I wonder why this warning was triggered. Unless you used
> "changeLJPair" in ParmEd (or somehow otherwise manually changed the
> LENNARD_JONES_ACOEF or BCOEF elements of the topology file, this should not
> be an issue.
> >
> > I noticed that the previous post was also about a protein coordinated to
> zinc. Does the new parameters derived from mcpb.py somehow trigger this
> warning?
> > Should I worry about it or can I use the prmtop and rst7 for
> minimization?
> >
> > Kind regards
> >
> > Lizelle Lubbe
> >
> > PhD (Medical biochemistry) candidate
> > Department of Integrative Biomedical Sciences
> > University of Cape Town
> > Disclaimer - University of Cape Town This e-mail is subject to UCT
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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--
Jason M. Swails
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Received on Sun Jul 23 2017 - 21:00:03 PDT
