AMBER Archive (2008)

Subject: Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Jul 31 2008 - 17:40:43 CDT

Hi,

I have not studied ff99 or ions08, but for ff94 in addition to
missing addAtomTypes there were also missing addPdbResMap and
addPdbAtomMap. We should get this right in future releases
by either including all these commands or by describing in comments
and in the manual why we didn't and what the user needs to do.

Here's DOCK's leaprc.dock.ions:
(http://dock.compbio.ucsf.edu/DOCK_6/index.htm)

# DOCK Amber Score Ion Library
# Scott Brozell March 2007

# Use Amber's ions94 library.
# It creates residues and units for alkali metal ions using ff94
# atom types and parameters defined in parm94.
# The Li+..Cs+ series uses information derived from the work of Aqvist.
# This information is identical to DOCK's vdw_AMBER_parm99.defn.
# ions94 also creates divalent, monoatomic ions for Mg, Ca, and Zn,
# but complete atom types and parameters are not in parm94;
# sensibly, the names chosen, MG, CA, and ZN, correspond to the
# common names of these ions in pdb's.

# Make the common names of these ions in pdb's recognizable to LEaP.
# IMO Amber is broken here - these commands should be in leaprc.ff94
addPdbResMap {
  { "LI" "Li+" } { 0 "LI" "Li+" } { 1 "LI" "Li+" }
  { "NA" "CIO" } { 0 "NA" "CIO" } { 1 "NA" "CIO" }
  { "K" "K+" } { 0 "K" "K+" } { 1 "K" "K+" }
  { "RB" "Rb+" } { 0 "RB" "Rb+" } { 1 "RB" "Rb+" }
  { "CS" "Cs+" } { 0 "CS" "Cs+" } { 1 "CS" "Cs+" }
}
addPdbAtomMap {
  { "LI" "Li+" }
  { "NA" "Na+" }
  { "K" "K+" }
  { "RB" "Rb+" }
  { "CS" "Cs+" }
}

# This merely prevents unknown atom type and maybe hybridization
# comments from LEaP. The application of this command is not thorough.
addAtomTypes {
   { "Mg" "Mg" "sp3" }
   { "Ca" "Ca" "sp3" }
   { "Sr" "Sr" "sp3" }
   { "Ba" "Ba" "sp3" }
   { "Sr" "Sr" "sp3" }
   { "V" "V" "sp3" }
   { "Zn" "Zn" "sp3" }
}

# Define the atom types and parameters for the alkaline earth ions
# and others; residues and units for some of these have not been created.
dock_ions = loadamberparams frcmod.dock.ions

# Use Amber's GAFF via mol2 and frcmod files for non-atomic ions.
# ACT acetate -1
ACT=loadmol2 act.mol2
frcmod=loadamberparams act.frcmod
# SO4 sulfate -2
SO4=loadmol2 so4.mol2
frcmod=loadamberparams so4.frcmod

# Treat magnesium with six waters as a single cation via water stripping.
addPdbResMap {
  { "MO6" "MG" } { 0 "MO6" "MG" } { 1 "MO6" "MG" }
}

Here's DOCK's frcmod.dock.ions:
DOCK Amber Score Ion Library
MASS
MG 24.305
Mg 24.305
Ca 40.08
Sr 87.62
Ba 137.34
V 50.9414
Fe 55.847
Zn 65.38

BOND

ANGLE

DIHE

IMPROPER

NONBON
  MG 0.787 0.875 DOCK vdw_AMBER_parm99.defn
  Mg 0.787 0.875 DOCK vdw_AMBER_parm99.defn
  Ca 1.326 0.4497 DOCK vdw_AMBER_parm99.defn
  Sr 1.742 0.118 DOCK vdw_AMBER_parm99.defn
  Ba 2.124 0.047 DOCK vdw_AMBER_parm99.defn
  V 2.100 0.320 DOCK vdw_AMBER_parm99.defn
  Fe 1.2 0.05 DOCK vdw_AMBER_parm99.defn
  Zn 1.10 0.0125 DOCK vdw_AMBER_parm99.defn

Scott

On Fri, 11 Jul 2008, Jeff Schwinefus wrote:

> Thank you both for your help. rdparm does indeed indicate the correct
> vdw parameters in my prmtop file. Interestingly, I found this in the
> first part of my leap.log file:
>
> > parm99 = loadamberparams parm99.dat
> Loading parameters: /home/apps/amber9/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: IM)
> (UNKNOWN ATOM TYPE: Li)
> (UNKNOWN ATOM TYPE: IP)
> (UNKNOWN ATOM TYPE: K)
> (UNKNOWN ATOM TYPE: Rb)
> (UNKNOWN ATOM TYPE: Cs)
> (UNKNOWN ATOM TYPE: Zn)
> (UNKNOWN ATOM TYPE: IB)
> (UNKNOWN ATOM TYPE: LP)
>
> It appears leaprc.ff99 does indeed not list these under addatomtypes.
> Thanks again.
>
> Jeff
>
> David A. Case wrote:
> > On Thu, Jul 10, 2008, Thomas Cheatham III wrote:
> >
> >> ...
> >>
> >>> (UNKNOWN ATOM TYPE: Li+)
> >>> (UNKNOWN ATOM TYPE: Na+)
> >>> (UNKNOWN ATOM TYPE: K+)
> >>> (UNKNOWN ATOM TYPE: Rb+)
> >>> (UNKNOWN ATOM TYPE: Cs+)
> >>> (UNKNOWN ATOM TYPE: F-)
> >>> (UNKNOWN ATOM TYPE: Cl-)
> >>> (UNKNOWN ATOM TYPE: Br-)
> >>> (UNKNOWN ATOM TYPE: I-)
> >>>
> >
> > I think you just need to have the appropriate lines in the addAtomTypes
> > lines in leaprc files. And I don't think the lack of such lines causes
> > any problems, but it is good to double-check that.
> >
> > ...dac

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