Hello,
I am having problems getting the SPCFW water working. The following are my
steps in tleap (I have added "…." To keep the file short):
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff03 (Duan et al.) force field
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "H" "H" "sp3" }
….
>> { "FE" "Fe" "sp3" }
>> # things should be there
>> { "IM" "Cl" "sp3" }
….
>> { "IB" "Na" "sp3" }
>> # "new" types
>> { "H0" "H" "sp3" }
>>
>> }
>> #
>> # Load the main parameter set.
>> #
>> parm99 = loadamberparams parm99.dat
Loading parameters:
/home/na3m/Download/AMBER10/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: LP)
>> frcmod03 = loadamberparams frcmod.ff03
Loading parameters:
/home/na3m/Download/AMBER10/amber10/dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
>>
>> #
>> # Load water and ions
>> #
>> loadOff ions94.lib
Loading library: /home/na3m/Download/AMBER10/amber10/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
….
Loading: Rb+
>> loadOff solvents.lib
Loading library:
/home/na3m/Download/AMBER10/amber10/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>> HOH = TP3
>> WAT = TP3
>>
>> #
>> # Load the existing 94 lib for nucleic acids and C- and N- terminal
groups
>> #
>> #
>> # Load DNA/RNA libraries
>> #
>> loadOff all_nucleic94.lib
Loading library:
/home/na3m/Download/AMBER10/amber10/dat/leap/lib/all_nucleic94.lib
Loading: DA
….
Loading: RUN
>> #
>> # Load main chain and terminating
>> # amino acid libraries.
>> #
>> loadOff all_aminoct94.lib
Loading library:
/home/na3m/Download/AMBER10/amber10/dat/leap/lib/all_aminoct94.lib
Loading: CALA
….
>> loadOff all_aminont94.lib
Loading library:
/home/na3m/Download/AMBER10/amber10/dat/leap/lib/all_aminont94.lib
Loading: ACE
….
>> loadOff all_amino03.lib
Loading library:
/home/na3m/Download/AMBER10/amber10/dat/leap/lib/all_amino03.lib
Loading: ACE
….
>>
>> #
>> # Define the PDB name map for the amino acids and DNA.
>> #
>> addPdbResMap {
>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
….
>> { 1 "T3" "DT3" }
>>
>> }
>>
>> addPdbAtomMap {
>> { "O5*" "O5'" }
….
>> # old ff atom names -> new
>> { "O1'" "O4'" }
>> { "OA" "O1P" }
>> { "OB" "O2P" }
>> }
>>
>>
>> #
>> # assumed that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>
> WAT = SPF
> set WAT.1 name "SPF"
> loadAmberParams frcmod.spcfw
Loading parameters:
/home/na3m/Download/AMBER10/amber10/dat/leap/parm/frcmod.spcfw
Reading force field modification type file (frcmod)
Reading title:
Parameter set for SPC/Fw of Wu, Tepper & Voth, J. Chem. Phys. 124:024503,
2006.
> set default FlexibleWater on
> 2trx = loadpdb 2trx.pdb
Loading PDB file: ./2trx.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue SER, term: Terminal/beginning, seq. number: 0 to: NSER.
(Residue 1: ASP, Nonterminal, was not found in name map.)
….
(Residue 106: LEU, Nonterminal, was not found in name map.)
Mapped residue ALA, term: Terminal/last, seq. number: 107 to: CALA.
Joining NSER - ASP
….
Joining LEU - CALA
total atoms in file: 822
Leap added 832 missing atoms according to residue templates:
832 H / lone pairs
> bond 2trx.35.SG 2trx.32.SG
> solvateBox 2trx SPCFWBOX 8
Solute vdw bounding box: 32.421 37.765 37.628
Total bounding box for atom centers: 48.421 53.765 53.628
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 3 y= 3 z= 3
Adding box at: x=0 y=0 z=0
Center of solvent box is: 18.774349, 18.774349, 18.774349
….
Center of solvent box is: -18.774349, -18.774349, -18.774349
Total vdw box size: 51.644 56.626 56.564 angstroms.
Volume: 165417.554 A^3
Total mass 74707.420 amu, Density 0.750 g/cc
Added 3499 residues.
> saveamberparm 2trx bbprotein.prmtop bbprotein.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -4.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
total 303 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
CALA 1
NSER 1
WAT 3499
)
(no restraints)
> quit
Quit
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This is my output file:
&cntrl
imin=1, maxcyc=1000, ncyc = 500,
cut=10.0,
ntpr=100, ntx=1, ntb=1, ntr = 1,
restraint_wt=5.0,
restraintmask=':1-108'
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 25.822
| New format PARM file being parsed.
| Version = 1.000 Date = 10/27/08 Time = 22:23:13
NATOM = 12151 NTYPES = 16 NBONH = 7830 MBONA = 838
NTHETH = 5410 MTHETA = 1138 NPHIH = 3595 MPHIA = 2681
NHPARM = 0 NPARM = 0 NNB = 23191 NRES = 3607
NBONA = 838 NTHETA = 1138 NPHIA = 2681 NUMBND = 42
NUMANG = 93 NPTRA = 50 NATYP = 29 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 851095
| Hollerith 76515
| Integer 402396
| Max Pairs 6998976
| nblistReal 145812
| nblist Int 511062
| Total 38995 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
Energy minimization:
maxcyc = 1000, ncyc = 500, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 51.644 Box Y = 56.626 Box Z = 56.564
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 54 NFFT2 = 60 NFFT3 = 60
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
Mask :1-108; matches 1654 atoms
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3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Error: A residue defined as a "fast 3-point water"
is not defined by a triangle of three bonds.
Residue 109 contains 2 bonds.
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I am not sure what I need to change. In my prmtop none of my commands about
changing the WAT to SPF are implemented. Any help would be appreciated.
Thanks
Naser
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Received on Wed Oct 29 2008 - 05:09:24 PDT
