Dear All,
I want to run a MD run with a protein containing Phosphothreonine but I have yet not been able to run it successfully. I am unable to save prmtop and inpcrd files.
Here are some details
This is how Phosphothreonine is present in my PDB file. I have already renamed Phosphothreonine residue to T1P in my PDB file.
HETATM 1271 N T1P A 160 3.866 54.370 75.593 1.00 39.63 N
HETATM 1272 CA T1P A 160 2.527 54.321 75.039 1.00 40.64 C
HETATM 1273 CB T1P A 160 2.607 54.481 73.505 1.00 40.07 C
HETATM 1274 CG2 T1P A 160 1.216 54.558 72.903 1.00 36.79 C
HETATM 1275 OG1 T1P A 160 3.316 55.690 73.198 1.00 38.51 O
HETATM 1276 P T1P A 160 4.682 55.669 72.505 1.00 37.43 P
HETATM 1277 O1P T1P A 160 5.230 57.069 72.503 1.00 37.01 O
HETATM 1278 O2P T1P A 160 5.495 54.658 73.289 1.00 34.97 O
HETATM 1279 O3P T1P A 160 4.314 55.216 71.156 1.00 33.48 O
HETATM 1280 C T1P A 160 1.802 53.010 75.352 1.00 43.78 C
HETATM 1281 O T1P A 160 2.344 51.924 75.141 1.00 43.08 O
Same residue name T1P (phosphothreonine with single protonated phosphate group, THR-PO2(OH) ) is used in the OFF file and FRCMOD file available for download via
http://www.pharmacy.manchester.ac.uk/bryce/amber
Now what I am doing step by step.
1. I am starting tLeap
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
-I: Adding /usr/local/amber10/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /usr/local/amber10//dat/leap/cmd/leaprc.ff99SB.
Welcome to LEaP!
Sourcing: /usr/local/amber10//dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /usr/local/amber10/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/amber10/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/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
2. Loading the off file for T1P
> loadoff T1P.off
Loading library: ./T1P.off
3. Loading the parameters file
> loadamberparams t1p.frcmod
Loading parameters: ./t1p.frcmod
Reading force field modification type file (frcmod)
Reading title:
# Parameters for THR-PO2(OH) : T1P; N.Homeyer, A.H.C.Horn, H.Lanig, H.Sticht, J. Mol. Model., in press
4. Loading my PDB file
> SAMP= loadpdb my.pdb
Loading PDB file: ./my.pdb
Created a new atom named: OG1 within residue: .R<T1P 160>
Added missing heavy atom: .R<T1P 160>.A<OG 11>
total atoms in file: 2383
Leap added 2427 missing atoms according to residue templates:
1 Heavy
2426 H / lone pairs
The file contained 1 atoms not in residue templates
5. Adding solvate box
> solvatebox SAMP TIP3PBOX 12.0
(using default radius 1.500000 for OG1)
(using default radius 1.500000 for OG1)
Solute vdw bounding box: 208.392 108.825 74.513
Total bounding box for atom centers: 232.392 132.825 98.513
Solvent unit box: 18.774 18.774 18.774
(using default radius 1.500000 for OG1)
(using default radius 1.500000 for OG1)
Total vdw box size: 235.430 135.763 101.289 angstroms.
Volume: 3237459.175 A^3
Mass > 1742666.444 amu, Density > 0.894 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 92983 residues.
6. Adding counter ions
> addions SAMP Cl- 0
4 Cl- ions required to neutralize.
Adding 4 counter ions to "SAMP" using 1A grid
Used default radius 1.50 for 2 atoms
Grid extends from solute vdw + 2.47 to 8.57
Resolution: 1.00 Angstrom.
grid build: 1 sec
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 107 sec
(Replacing solvent molecule)
Placed Cl- in SAMP at (85.15, -47.34, 1.26).
(Replacing solvent molecule)
Placed Cl- in SAMP at (-86.57, 35.03, -28.30).
(Replacing solvent molecule)
Placed Cl- in SAMP at (79.28, -49.21, 2.32).
(Replacing solvent molecule)
Placed Cl- in SAMP at (-71.65, 35.88, 6.37).
7. Saving amber parmeters
> saveamberparm SAMP SAMP.prmtop SAMP.inpcrd
Checking Unit.
WARNING: There is a bond of 3.550979 angstroms between:
------- .R<T1P 160>.A<CB 5> and .R<T1P 160>.A<OG 11>
WARNING: There is a bond of 3.550980 angstroms between:
------- .R<T1P 456>.A<OG 11> and .R<T1P 456>.A<CB 5>
FATAL: Atom .R<T1P 160>.A<OG1 19> does not have a type.
FATAL: Atom .R<T1P 456>.A<OG1 19> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Please help me to solve this problem. I am in the initial stages of learning amber. I am also curious to know that on
http://www.pharmacy.manchester.ac.uk/bryce/amber there are three entries for Phosphothreonine and the third entry does not have any corresponding FRCMOD file but on a OFF file
With Regards
Imtiaz
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Received on Wed Jan 27 2010 - 02:30:08 PST
