Dear All,
I am trying to load amber compatible HEM parameter from a 2011 paper
<
https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21922>.
But I'm getting error after loading the pdb file.
I have tried setting the FE atom-type and bonding the Fe-S-Cys, but I'm
unable to understand the correct syntax for specifying atoms/residues/unit.
Can you please take a look at the following tleap output and suggest how to
modify the tleap script?
desc command seems to suggest something is wrong.
PDB file is attached for reference and tleap script below.
Also forgot the command to find the total charge on a unit, can't find it
quickly in the manual after searching "charge command".
thank you.
tleap script
--------------
source leaprc.constph
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
loadamberparams HEM_HS.frcmod
HEM = loadmol2 HEM.mol2
CYP = loadmol2 CYS_HS.mol2
1W0E = loadpdb 1W0E_amber18.pdb
set 1W0E.A1501.43 element "Fe"
bond 1W0E.A1501.43 1W0E.420.3408 #BOND CYS-S to HEM-FE
#set 2j2.405 connect0 2j2.405.1
#set 2j2.405 connect1 2j2.405.9
bond 1W0E.419.C 1W0E.420.N #BOND CYS to the protein (new CYP residue)
bond 1W0E.420.C 1W0E.421.N #As above
-------------------------
tleap output
----------------
[r11831vd.hlogin1 [csf3] 3A4]$ tleap
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/prep to
search path.
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib to
search path.
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm to
search path.
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd to
search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.constph
----- Source:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/leaprc.constph
----- Source of
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/leaprc.constph
done
----- Source:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/oldff/leaprc.ff10
----- Source of
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/oldff/leaprc.ff10
done
Log file: ./leap.log
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/amino10.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/aminoct10.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/aminont10.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/oldff/phosphoaa10.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/nucleic10.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/atomic_ions.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/solvents.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/constph.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/all_prot_nucleic10.lib
Loading library:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib/cph_nucleic_caps.lib
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/frcmod.constph
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for titrations
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/frcmod.protonated_nucleic
Reading force field modification type file (frcmod)
Reading title:
Force field modifications for protonated nucleic acids
Using H(N)-modified Bondi radii
> source leaprc.gaff
----- Source:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/leaprc.gaff
----- Source of
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
> loadamberparams HEM_HS.frcmod
Loading parameters: ./HEM_HS.frcmod
Reading force field modification type file (frcmod)
Reading title:
Ferric-high-spin.frcmod- Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III,
T.E. Jour Comp Chem (2011)
> HEM = loadmol2 HEM.mol2
Loading Mol2 file: ./HEM.mol2
Reading MOLECULE named HEM-IC6
> CYP = loadmol2 CYS_HS.mol2
Loading Mol2 file: ./CYS_HS.mol2
Reading MOLECULE named CYP-IC6
> 1W0E = loadpdb 1W0E_amber18.pdb
Loading PDB file: ./1W0E_amber18.pdb
(starting new molecule for chain )
+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
Created a new atom named: ND2 within residue: .R<AS4 1917>
Added missing heavy atom: .R<AS4 1917>.A<OD2 10>
Warning: One sided connection. Residue (CYP-IC6) missing connect0 atom.
Warning: One sided connection. Residue (default_name) missing connect1 atom.
total atoms in file: 3844
Leap added 3917 missing atoms according to residue templates:
1 Heavy
3916 H / lone pairs
The file contained 1 atoms not in residue templates
> set 1W0E.A1501.43 element "Fe"
Error: 1W0E.A1501.43: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set 1W0E.A1501.43 element Fe
Error: 1W0E.A1501.43: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> bond 1W0E.A1501.43 1W0E.420.3408
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 43 3408 1
Error: bond: Argument #1 is type Double must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 1W0E.A1501.43 1W0E.420.3408 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond FE SG 1
Error: bond: Argument #1 is type Unit must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 1W0E.A1501.FE 1W0E.420.SG 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> set 1W0E.A1501.43 element "FE"
Error: 1W0E.A1501.43: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set 1W0E.A1501.43 element FE
Error: 1W0E.A1501.43: not a container (e.g. residue)
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> bond 1W0E.43.FE 1W0E.3408.SG 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 1W0E.43.FE 1W0E.3403.SG 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 43 340~38 1
Error: bond: Argument #1 is type Double must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 43 3403 1
Error: bond: Argument #1 is type Double must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond SG FE 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 1W0ESG.3403 1W0E.FE.43 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond 1W0E.SG.3403 1W0E.FE.43 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> bond SG.3403 FE.43 1
Error: bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
> desc 1W0E.43.FE
STRING (with no reference): '1W0E.43.FE'
> desc 1W0E.3403.SG
STRING (with no reference): '1W0E.3403.SG'
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Wed May 29 2019 - 08:00:03 PDT
