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
>
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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 Thu Jul 13 2017 - 04:00:03 PDT
