Dear All,
Please suggest on this one sided connection warning. Can I start my MD
simulations ignoring this error or my prmtop/inpcrd files have errors which
I should fix first? If so, how? Thanks in advance.
On Sun, Mar 24, 2013 at 11:23 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote:
> Dear Dr. Jason and Amber people,
> Thanks for your suggestion given here,
> http://archive.ambermd.org/201303/0168.html and associated threads.
> I have followed your suggestions and found that when I added charges of
> CYP and HEM units, they summed up to exactly 2.000. CYP is a modified
> unit for CYS435 residue.
> Then I have connected the S and Fe atoms with the command "bond
> 2vn0.435.SG <http://2vn0.435.sg/> 2vn0.492.FE" and it seems to have
> worked as seen in the snapshot of prmtop and inpcrd loaded in VMD
> (attached).
> There was "one sided connection" warning for which a search suggested that
> I should add TER card before and after CYP, but since it is part of the
> protein chain, I did not add any TER card in the pdb.
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section2.htm
>
> Please find time to suggest if the input files that I have generated here
> are compatible for starting a meaningful MD simulation or there
> are warnings/errors which I should be taking care of before starting any MD
> on these prmtop and inpcrd files.
>
> Thanks again for your valuable inputs.
> gm.linux-rfml:~/Documents/MD/CYP450/TGZ_2vn0> tleap -s -f leap_TGZ.in
> -I: Adding /usr/local/amber12/dat/leap/prep to search path.
> -I: Adding /usr/local/amber12/dat/leap/lib to search path.
> -I: Adding /usr/local/amber12/dat/leap/parm to search path.
> -I: Adding /usr/local/amber12/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source leap_TGZ.in.
>
> Welcome to LEaP!
> Sourcing: ./leap_TGZ.in
> ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.ff99SB done
> Log file: ./leap.log
> Loading parameters: /usr/local/amber12/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /usr/local/amber12/dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/amber12/dat/leap/lib/all_amino94.lib
> Loading library: /usr/local/amber12/dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/amber12/dat/leap/lib/all_aminont94.lib
> Loading library: /usr/local/amber12/dat/leap/lib/ions94.lib
> Loading library: /usr/local/amber12/dat/leap/lib/solvents.lib
> ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff
> ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> add. info. at the end
> Loading Mol2 file: ./CYP.mol2
> Reading MOLECULE named CYP-IC6
>
> Loading parameters: ./Heme.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Loading Mol2 file: ./Heme.mol2
> Reading MOLECULE named HEM
> Loading PDB file: ./2VN0_heme2.pdb
> One sided connection. Residue: CYP-IC6 missing connect0 atom.
> One sided connection. Residue: default_name missing connect1 atom.
>
> Added missing heavy atom: .R<CHIE 491>.A<OXT 18>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NB-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NA-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-ND-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NC-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> total atoms in file: 7491
> Leap added 11 missing atoms according to residue templates:
> 1 Heavy
> 10 H / lone pairs
> > bond 2vn0.435.SG <http://2vn0.435.sg/> 2vn0.492.FE
> > check CYP
> Checking 'CYP'....
> ERROR: The unperturbed charge of the unit: -0.402400 is not integral.
> WARNING: The unperturbed charge of the unit: -0.402400 is not zero.
> Checking parameters for unit 'CYP'.
>
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warnings: 1
> > check HEM
> Checking 'HEM'....
> ERROR: The unperturbed charge of the unit: -1.597600 is not integral.
> WARNING: The unperturbed charge of the unit: -1.597600 is not zero.
> Checking parameters for unit 'HEM'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warnings: 1
> > charge 2vn0
> Total unperturbed charge: 4.000000
> Total perturbed charge: 4.000000
> > addions 2vn0 Cl- 0
> 4 Cl- ions required to neutralize.
> Adding 4 counter ions to "2vn0" using 1A grid
> Grid extends from solute vdw + 2.47 to 8.47
> Resolution: 1.00 Angstrom.
> grid build: 1 sec
> (no solvent present)
> Calculating grid charges
> charges: 10 sec
> Placed Cl- in 2vn0 at (64.02, 27.80, 6.36).
> Placed Cl- in 2vn0 at (33.02, 6.80, -17.64).
> Placed Cl- in 2vn0 at (71.02, 17.80, -17.64).
> Placed Cl- in 2vn0 at (43.02, -2.20, -36.64).
>
> Done adding ions.
> > solvateoct 2vn0 TIP3PBOX 8.0
> Scaling up box by a factor of 1.346722 to meet diagonal cut criterion
> Solute vdw bounding box: 67.160 51.455 74.221
> Total bounding box for atom centers: 95.768 95.768 95.768
> (box expansion for 'iso' is 41.6%)
> Solvent unit box: 18.774 18.774 18.774
> Volume: 453071.057 A^3 (oct)
> Total mass 244848.466 amu, Density 0.897 g/cc
> Added 10626 residues.
> > saveamberparm 2vn0 2vn0_apo.prmtop 2vn0_apo.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 1473 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
>
> res total affected
>
> CHIE 1
> CYP 1
> HEM 1
> NLYS 1
> WAT 10626
> )
> (no restraints)
> >
> > check 2vn0
> Checking '2vn0'....
> Warning: Close contact of 1.430419 angstroms between .R<NLYS 28>.A<HD3
> 15> and .R<NLYS 28>.A<H3 4>
> Warning: Close contact of 1.493880 angstroms between .R<NLYS 28>.A<HD3
> 15> and .R<NLYS 28>.A<H1 2>
> Warning: Close contact of 0.109243 angstroms between .R<NLYS 28>.A<H3 4>
> and .R<NLYS 28>.A<H1 2>
> Warning: Close contact of 1.313180 angstroms between .R<ILE 38>.A<HG23
> 10> and .R<ILE 39>.A<HG23 10>
> Warning: Close contact of 1.454352 angstroms between .R<LYS 118>.A<HZ1
> 18> and .R<LYS 279>.A<HD3 13>
> Warning: Close contact of 1.314590 angstroms between .R<MET 136>.A<HE3
> 15> and .R<ASP 262>.A<HA 4>
> Warning: Close contact of 1.421075 angstroms between .R<ILE 141>.A<HA 4>
> and .R<ARG 144>.A<HD2 12>
> Warning: Close contact of 1.299580 angstroms between .R<PRO 166>.A<HB2 9>
> and .R<LEU 170>.A<HD22 16>
> Warning: Close contact of 1.401001 angstroms between .R<LEU 170>.A<HD21
> 15> and .R<LEU 310>.A<HD12 12>
> Warning: Close contact of 1.412214 angstroms between .R<ALA 173>.A<HB3 8>
> and .R<PRO 174>.A<HD2 3>
> Warning: Close contact of 1.461887 angstroms between .R<ARG 261>.A<HE 15>
> and .R<ASP 265>.A<OD2 10>
> Warning: Close contact of 1.172415 angstroms between .R<ILE 331>.A<HD13
> 17> and .R<PRO 337>.A<HB3 10>
> Warning: Close contact of 1.024731 angstroms between .R<LYS 415>.A<HD2
> 12> and .R<LYS 415>.A<H 2>
> Warning: Close contact of 1.332051 angstroms between .R<ILE 434>.A<C 18>
> and .R<CYP 435>.A<N 1>
> Warning: Close contact of 1.326672 angstroms between .R<CYP 435>.A<C 9>
> and .R<ALA 436>.A<N 1>
> Checking parameters for unit '2vn0'.
>
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 15
> Unit is OK.
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D.
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408, +91-7709129400.
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Thu Mar 28 2013 - 22:30:03 PDT
