Hi,
I guess I can help. I have a phosphothreonine in my protein as well, I got
similar error about atom types, I just changed the atom type in the pdb and
re ran leap, it worked.. Try doing this
Soumya
On Wed, Jan 27, 2010 at 3:48 PM, MUHAMMAD IMTIA SHAFIQ <
imtiazshafiq.gmail.com> wrote:
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 27 2010 - 05:00:02 PST
