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
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Received on Wed Jul 12 2017 - 05:30:04 PDT
