If you're not python-averse, one thing you could potentially do is
edit $AMBERHOME/AmberTools/src/parmed/parmed/tools/checkvalidity.py
and make the off-diagonal warning more verbose so you can see exactly
which types/parameters are causing the message to trigger (it's around
line 182 in my version but just search for the text "Modified").
-Dan
On Sun, Jul 23, 2017 at 11:30 PM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> 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
>> policies and e-mail disclaimer published on our website at
>> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27
>> 21 650 9111. If this e-mail is not related to the business of UCT, it is
>> sent by the sender in an individual capacity. Please report security
>> incidents or abuse via csirt.uct.ac.za
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>> Disclaimer - University of Cape Town This e-mail is subject to UCT
>> policies and e-mail disclaimer published on our website at
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>> 21 650 9111. If this e-mail is not related to the business of UCT, it is
>> sent by the sender in an individual capacity. Please report security
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>>
>
>
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za
> _______________________________________________
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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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Received on Mon Jul 24 2017 - 06:00:06 PDT
