Thanks for the reply Pengfei.
I have since started simulations without applying these improper terms and they are running better. The metal was not in an exact plane with the initial conformation of the one Histidine ring which caused distortion when trying to apply the impropers while the solute is restrained
Regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
________________________________________
From: Pengfei Li <ambermailpengfei.gmail.com>
Sent: 20 September 2017 04:20:45 AM
To: AMBER Mailing List
Subject: Re: [AMBER] improper torsion terms
Hi Lizelle,
“printBonds", “printAngles”, and “printDihedrals" commands in ParmEd may help.
Kind regards,
Pengfei
> On Sep 18, 2017, at 11:07 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
>
> Dear All,
>
> I am trying to minimize a glycosylated metalloprotein and prepared the prmtop and rst7 using tleap and forcefield parameters of the active site zinc ion coordination from Bras et al (2014) dx.doi.org/10.1021/cs500093h; ACS Catal. 2014, 4, 2587−2597. The Zn is coordinated to a water molecule, 2 histidines and a glutamate.
>
> tleap gave warnings about missing improper torsion terms and I noticed that the glutamate OE1 is amongst them (which I'm guessing is alright?). The histidine NE2's are not mentioned. Parmed.py checks out fine after SetMolecules was used and the output from printDetails of metal site residues also looks fine.
> After centering the molecule with cpptraj these files were used as input for minimization.
>
> Here is my frcmod file (NK is for HIR361 (Histidine), NN is for HIT365 (Histidine), ON is for GLR389 (glutamate) and OK for WAR (TIP3P water):
>
> REMARK, FORCEFIELD PARAMETERS OF ZINC SITE TAKEN FROM BRAS ET AL
> MASS
> NK 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
> NN 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
> ON 16.00 carboxyl and phosphonate group oxygen
> OK 16.00 oxygen in tip3p water
> Z1 65.40 zinc ion
>
> BOND
> NK-CR 488.0 1.335 JCC,7,(1986),230; HIS
> NK-Z1 106.49 1.997 Bras
> CV-NK 410.0 1.394 JCC,7,(1986),230; HIS
> NN-CR 488.0 1.335 JCC,7,(1986),230; HIS
> NN-Z1 88.07 2.029 Bras
> CV-NN 410.0 1.394 JCC,7,(1986),230; HIS
> ON-Z1 105.73 1.959 Bras
> ON-C 656.0 1.250 JCC,7,(1986),230;GLU,ASP
> OK-Z1 66.54 2.056 Bras
> OK-HW 553.0 0.9572 TIP3P water
>
> ANGL
> NK-Z1-NN 36.12 112.53 Bras
> NK-Z1-OK 17.73 137.14 Bras
> NK-Z1-ON 64.70 95.65 Bras
> NN-Z1-ON 26.27 115.04 Bras
> NN-Z1-OK 26.93 99.83 Bras
> OK-Z1-ON 46.96 95.20 Bras
> CV-NN-Z1 26.5 130.48 Tuccinardi,2006 Angle Bras
> CR-NN-Z1 26.5 122.56 Tuccinardi,2006 Angle Bras
> CR-NK-Z1 26.5 113.83 Tuccinardi,2006 Angle Bras
> CV-NK-Z1 26.5 134.21 Tuccinardi,2006 Angle Bras
> Z1-OK-HW 35.47 92.69 Bras
> C -ON-Z1 27.59 117.23 Bras
> H4-CV-NN 50.0 120.00 amber
> NN-CV-CC 70.0 120.00 amber
> NN-CR-H5 50.0 120.00 amber
> NN-CR-NA 70.0 120.00 amber
> CV-NN-CR 70.0 117.00 amber
> H4-CV-NK 50.0 120.00 amber
> NK-CV-CC 70.0 120.00 amber
> NK-CR-H5 50.0 120.00 amber
> NK-CR-NA 70.0 120.00 amber
> CV-NK-CR 70.0 117.00 amber
> CT-C -ON 70.0 117.00 amber
> O2-C -ON 80.0 126.00 amber (AA GLU(SCH JPC 79,2379))
> HW-OK-HW 100.0 104.52 amber TIP3p water
> HW-HW-OK 0.0 127.74 amber (crystallographic water with 3 bonds)
>
> DIHE
> CC-CV-NN-Z1 1 0.0 180.0 1.0
> NA-CR-NN-Z1 1 0.0 180.0 1.0
> CR-NN-Z1-NK 1 0.0 180.0 1.0
> CR-NN-Z1-OK 1 0.0 180.0 1.0
> H5-CR-NN-Z1 1 0.0 180.0 1.0
> NN-Z1-NK-CV 1 0.0 180.0 1.0
> NN-Z1-NK-CR 1 0.0 180.0 1.0
> NN-Z1-OK-CV 1 0.0 180.0 1.0
> NN-Z1-OK-CR 1 0.0 180.0 1.0
> CC-CV-NK-Z1 1 0.0 180.0 1.0
> NA-CR-NK-Z1 1 0.0 180.0 1.0
> CR-NK-Z1-ON 1 0.0 180.0 1.0
> H5-CR-NK-Z1 1 0.0 180.0 1.0
> CR-NK-Z1-OK 1 0.0 180.0 1.0
> NK-Z1-NN-CV 1 0.0 180.0 1.0
> NK-Z1-ON-C 1 0.0 180.0 1.0
> NK-Z1-OK-HW 1 0.0 180.0 1.0
> CV-NK-Z1-ON 1 0.0 180.0 1.0
> CV-NK-Z1-OK 1 0.0 180.0 1.0
> H4-CV-NK-Z1 1 0.0 180.0 1.0
> CR-NN-Z1-ON 1 0.0 180.0 1.0
> NN-Z1-ON-C 1 0.0 180.0 1.0
> NN-Z1-OK-HW 1 0.0 180.0 1.0
> CV-NN-Z1-ON 1 0.0 180.0 1.0
> CV-NN-Z1-OK 1 0.0 180.0 1.0
> H4-CV-NN-Z1 1 0.0 180.0 1.0
> CT-C-ON-Z1 1 0.0 180.0 1.0
> C-ON-Z1-OK 1 0.0 180.0 1.0
> ON-Z1-OK-HW 1 0.0 180.0 1.0
> O2-C-ON-Z1 1 0.0 180.0 1.0
> Z1-OK-HW-HW 1 0.0 180.0 1.0
> CR-NN-CV-CC 2 4.80 180.0 2.0
> CV-NN-CR-H5 2 10.00 180.0 2.0
> CV-NN-CR-NA 2 10.00 180.0 2.0
> H4-CV-NN-CR 2 4.80 180.0 2.0
> CR-NK-CV-CC 2 4.80 180.0 2.0
> CV-NK-CR-H5 2 10.00 180.0 2.0
> CV-NK-CR-NA 2 10.00 180.0 2.0
> H4-CV-NK-CR 2 4.80 180.0 2.0
>
> IMPR
> CR-CV-Z1-NN 1 50.0 180.0 2.
> CV-CR-Z1-NN 1 50.0 180.0 2.
> CR-CV-Z1-NK 1 50.0 180.0 2.
> CV-CR-Z1-NK 1 50.0 180.0 2.
> CV-CR-NK-Z1 1 500.0 180.0 2.
> CV-CR-NN-Z1 1 500.0 180.0 2.
>
> NONB
> NK 1.8240 0.1700 Amber
> NN 1.8240 0.1700 Amber
> ON 1.6612 0.2100 Amber
> OK 1.7683 0.1520 Amber TIP3p water
> Z1 1.7000 0.0125 Amber (Ryde et al)
>
> I first minimized the metal site without SHAKE since my starting geometry did not exactly match the frcmod (min1). This worked out fine.
>
> Constant Volume Minimization 1 with all but metal site fixed SD only
> # Control section
> &cntrl
> imin=1,
> irest = 0,
> ntmin = 2, maxcyc = 500, dx0 = 0.01, drms = 0.0001,
> cut = 10.0,
> ntb = 1,
> ntp = 0,
> ntwx = 20,
> ntpr = 20,
> ntwr = 500,
> ioutfm = 1,
> iwrap = 1,
> ntr = 1, restraintmask='!:WAR,ZN1,HIR,HIT,GLR', restraint_wt=50.0
>
> /
>
> Thereafter I tried minimizing the solvent with the solute atoms restrained.
>
> Constant Volume Minimization 2 of solvent
> # Control section
> &cntrl
> imin=1,
> irest = 0,
> ntmin = 1, maxcyc = 5000, ncyc = 2500, dx0 = 0.01, drms = 0.0001,
> cut = 10.0,
> ntb = 1,
> ntp = 0,
> ntwx = 50,
> ntpr = 50,
> ntwr = 5000,
> ioutfm = 1,
> iwrap = 1,
> ntr = 1, restraintmask='!:WAT,Na+', restraint_wt=50.0
>
> /
>
> There are no errors but I noticed that despite the restraints the metal site's HIR and HIT NE2 atoms still move. They have bonds to the ZN and get pulled so that the histidine ring loses some planarity. Although I do see the waters moving slightly, for the most part in the min2.out the gmax is for these NE2 atoms and they are quite mobile. I'm worried that the minimizer is trying to optimize these atoms and not minimizing the solvent properly. Could someone please explain to me why they still move despite the restraint?
>
> Although tleap did not detect missing improper torsion terms for the NK and NN atoms of these histidines I think that perhaps the ones given in the frcmod file are not being read properly. Improper torsion terms would maintain the planarity of the sp2 bonds in the histidine rings right?
>
> I obtained this frcmod from the authors and noticed that the spacing of these lines differ. How could I confirm that they are being read? If this is not causing the strange behaviour what else could I check?
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Chemical Biology) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
> South Africa
> 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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Received on Wed Sep 20 2017 - 01:00:02 PDT
