AMBER Archive (2008)

Subject: AMBER: SPCFW problems

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Mon Oct 27 2008 - 21:37:12 CDT


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

**********************************************************

**********************************************************

**********************************************************

**********************************************************

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

--------------------------------------------------------------------------------

   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.

**********************************************************

**********************************************************

**********************************************************

**********************************************************

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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