Dear Amber users and developers,
I am trying to prepare prmtop and inpcrd files for MD with 1W0E structure.
For this I have taken HEM and CYS coordinates and parameters from SI of J.
Comp. Chem. 2012 33, 119 (attached).
I have prepared the PDB in Schrodinger package (attached) and used the
following set of commands to load coord. and parameters.
The HEM and CYX units don't seem to have problem but the leap complaints
about atom types of 9 H atoms in the protein, which is strange to me.
After the protein pdb is loaded it also gave some messages which are not
clear to me.
There also seems to be a problem while adding Cl- atoms to neutralize the
protein.
Can you please take a look and suggest me on fixing these issues?
Thank you.
ukmcdwlx005 121% tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
-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 /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99.
Welcome to LEaP!
Could not open file
/apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99: No such file
or directory
> source leaprc.ff99SB
----- 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 leaprc.gaff
----- 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
> HEM = loadmol2 HEM_pentacoordinateHS.mol2
Loading Mol2 file: ./HEM_pentacoordinateHS.mol2
Reading MOLECULE named HEM-IC6
> loadamberparams HEM_HS.frcmod
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?
> P450 = loadpdb 1W0E_prepared.pdb
Loading PDB file: ./1W0E_prepared.pdb
Created a new atom named: H within residue: .R<ACE 24>
Created a new atom named: H1 within residue: .R<TYR 25>
Created a new atom named: HE2 within residue: .R<GLU 97>
Created a new atom named: HD2 within residue: .R<ASP 270>
Created a new atom named: HE2 within residue: .R<GLU 320>
Created a new atom named: HD1 within residue: .R<HIE 324>
Created a new atom named: HD1 within residue: .R<HIE 402>
Created a new atom named: H1 within residue: .R<CTHR 499>
Created a new atom named: H2 within residue: .R<CTHR 499>
Added missing heavy atom: .R<CTHR 499>.A<CA 3>
Added missing heavy atom: .R<CTHR 499>.A<CB 5>
Added missing heavy atom: .R<CTHR 499>.A<C 13>
Added missing heavy atom: .R<CTHR 499>.A<CG2 7>
Added missing heavy atom: .R<CTHR 499>.A<OG1 11>
Added missing heavy atom: .R<CTHR 499>.A<O 14>
Added missing heavy atom: .R<CTHR 499>.A<OXT 15>
+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: 7791
Leap added 20 missing atoms according to residue templates:
7 Heavy
13 H / lone pairs
The file contained 9 atoms not in residue templates
> solvateoct P450 TIP3PBOX 12
Scaling up box by a factor of 1.277713 to meet diagonal cut criterion
Solute vdw bounding box: 48.126 79.499 73.246
Total bounding box for atom centers: 110.164 110.164 110.164
(box expansion for 'iso' is 48.2%)
Solvent unit box: 18.774 18.774 18.774
Volume: 686845.755 A^3 (oct)
Mass > 374698.160 amu, Density > 0.906 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 17745 residues.
> charge p450
charge: Argument #1 is type String must be of type: [unit molecule residue
atom list]
usage: charge <object>
> charge P450
Total unperturbed charge: 2.402400
Total perturbed charge: 2.402400
> addions P450 Cl- 0
2 Cl- ions required to neutralize.
Adding 2 counter ions to "P450" using 1A grid
Used default radius 1.50 for 9 atoms
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 (-3.34, 13.09, -20.93).
(Replacing solvent molecule)
Placed Cl- in P450 at (-21.84, 3.66, -12.39).
Done adding ions.
> saveamberparm P450 P450_1W0E.prmtop P450_1W0E.inpcrd
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.402400 is not integral.
WARNING: The unperturbed charge of the unit: 0.402400 is not zero.
FATAL: Atom .R<ACE 24>.A<H 7> does not have a type.
FATAL: Atom .R<TYR 25>.A<H1 22> does not have a type.
FATAL: Atom .R<GLU 97>.A<HE2 16> does not have a type.
FATAL: Atom .R<ASP 270>.A<HD2 13> does not have a type.
FATAL: Atom .R<GLU 320>.A<HE2 16> does not have a type.
FATAL: Atom .R<HIE 324>.A<HD1 18> does not have a type.
FATAL: Atom .R<HIE 402>.A<HD1 18> does not have a type.
FATAL: Atom .R<CTHR 499>.A<H1 16> does not have a type.
FATAL: Atom .R<CTHR 499>.A<H2 17> does not have a type.
Failed to generate parameters
Parameter file was not saved.
>
--
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 Tue Apr 07 2015 - 05:00:02 PDT
