Hi All,
I have followed the procedure suggested and used the following modified
leap input file and it seems to work except for the fact that bond between
S and Fe is not formed.
Can you please suggest on the correct usage for "bond" command? I have
tried "bond P450.6768.SG P450.7755.FE 1", "bond 6768 7755 1" but got the
same error message.
Thanks a lot.
Cheers.
Vaibhav
Leap.in
source leaprc.ff99SB
source leaprc.gaff
CYP = loadmol2 CYS_HS.mol2
set CYP head CYP.1.N
set CYP tail CYP.1.C
desc CYP
HEM = loadmol2 HEM_pentacoordinateHS.mol2
loadamberparams HEM_HS.frcmod
P450 = loadpdb 1W0E_P450_leap.pdb
bond <P450.6786.SG> <P450.7755.FE> [1]
solvateoct P450 TIP3PBOX 12
charge P450
addions P450 Cl- 0
ukmcdwlx005 129% tleap -s -f leap.in
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/prep to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/lib to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/parm to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap.in.
Welcome to LEaP!
Sourcing: ./leap.in
----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB
----- Source of
/apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_nucleic94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_amino94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminoct94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminont94.lib
Loading library: /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/ions94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/solvents.lib
----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
----- Source of /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/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: ./CYS_HS.mol2
Reading MOLECULE named CYP-IC6
UNIT name: CYP-IC6
Head atom: .R<CYP 1>.A<N 1>
Tail atom: .R<CYP 1>.A<C 9>
Contents:
R<CYP 1>
Loading Mol2 file: ./HEM_pentacoordinateHS.mol2
Reading MOLECULE named HEM-IC6
Loading parameters: ./HEM_HS.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading PDB file: ./1W0E_P450_leap.pdb
+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: 7800
*bond: Argument #1 is type Double must be of type: [atom]usage: bond
<atom1> <atom2> [order]*
Scaling up box by a factor of 1.278448 to meet diagonal cut criterion
Solute vdw bounding box: 79.806 73.249 48.124
Total bounding box for atom centers: 110.488 110.488 110.488
(box expansion for 'iso' is 49.0%)
Solvent unit box: 18.774 18.774 18.774
Volume: 692882.227 A^3 (oct)
Total mass 378175.248 amu, Density 0.906 g/cc
Added 17938 residues.
Total unperturbed charge: 2.000000
Total perturbed charge: 2.000000
2 Cl- ions required to neutralize.
Adding 2 counter ions to "P450" using 1A grid
Grid extends from solute vdw + 2.47 to 8.47
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 15 sec
(Replacing solvent molecule)
Placed Cl- in P450 at (14.09, 17.59, -12.81).
(Replacing solvent molecule)
Placed Cl- in P450 at (10.04, 18.54, 13.48).
Done adding ions.
> saveamberparm P450 P450_1W0E.prmtop P450_1W0E.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1497 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
ACE 1
CTHR 1
CYP 1
HEM 1
WAT 17936
)
(no restraints)
> saveamberparm P450 P450_1W0E.prmtop P450_1W0E.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1497 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
ACE 1
CTHR 1
CYP 1
HEM 1
WAT 17936
)
(no restraints)
>
On Tue, Apr 7, 2015 at 3:29 PM, Mark Williamson <mjw.mjw.name> wrote:
> On 07/04/15 12:54, Vaibhav Dixit wrote:
> > Loading parameters: ./HEM_HS.frcmod
> > Reading force field modification type file (frcmod)
> > Reading title:
> > remark goes here
> > Unknown keyword:
> > in parameter file. Perhaps a format error?
>
> 1) You (as attached anyway) have stray carriage return characters in
> some of your parameter files. Run:
>
> dos2unix HEM_HS.frcmod
> dos2unix HEM_pentacoordinateHS.mol2
>
> to fix this.
>
> 2) As Dave mentions, I would let leap build the topology as a function
> the (correct) PDB residue names, i.e. remove all hydrogens, and CONECT
> records before loading into leap. This is a fragile example that will
> probably work:
>
> grep -v " H " 1W0E_prepared.pdb.orig > a
> grep -v "CONECT" a > b
>
> 3) I would also indicate the HEM linked CYS residue by renaming it to
> match the resname in the CYP.mol file (CYP-IC6) of the SI of
> http://dx.doi.org/10.1002/jcc.21922
>
> sed s/CYX/CYS/g b > 1W0E_prepared.pdb
>
> and then ensure you have these extra bits in your leap script:
>
> CYP = loadMol2 CYP.mol2
>
> # Needed because mol2 does not contain head/tail info
> set CYP head CYP.1.N
> set CYP tail CYP.1.C
> desc CYP
>
> You will also need an extra "bond" command here in leap to link it with
> the iron atom in the HEM residue, since this was removed with the
> stripping of the CONECT records above.
>
> Regards,
>
> Mark
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 08 2015 - 09:00:02 PDT
