[gmx-users] Re: Parameters for AOT molecule/Too few parameters on line

[Mark Abraham]

On 2/04/2010 3:07 PM, Lum Nforbi wrote:
> Justin,
>
>     I appreciate your reply. Actually, I have read through the section
> of building parameter files in chap. 5 several times. The only reason
> for using atom types instead of numbers is because that is the way they
> are represented in the ffcharmmbon.itp and ffcharmmnb.itp files. Numbers
> are not used in these force fields. The [ bondtypes ] below is a portion
> of the [bondtypes ] listed in the ffcharmmbon.itp file. I will
> definitely use numbers.
>
> [ bondtypes ]
> ; i    j    func    b0    kb
> CST    OST    1    0.116    784884.928
> SS    FE    1    0.232    209200.0
> C    C    1    0.1335    502080.0
> CA    CA    1    0.1375    255224.0
> CE1    CE1    1    0.134    368192.0
> CE1    CE2    1    0.1342    418400.0
> CE1    CT2    1    0.1502    305432.0

I haven't followed this closely, but perhaps one or other of you has 
missed a point here. Even if not, perhaps this description will help 
others understand the way the .itp files work.

The [ (bond|angle|etc) ] sections require atom indices (i.e. indices 
into the [ atoms ] section) in which pdb2gmx has constructed a three-way 
mapping between atom index, atom type and atom name (with help from the 
.rtp database). grompp can then use this mapping from atom indices to 
atom types to find in the [ (bond|angle|etc)types ] sections the actual 
parameter data. Accordingly, the latter sections require atom types. The 
[ molecules section ] defines a list of [ moleculetypes ] so that grompp 
can also check that the atom ordering is sane, which requires the 
aforementioned mapping from atom indices to atom names.

Different force fields use different techniques for things like 
1,4-interaction-parameter generation, dihedral lookup and 
nonbonded-parameter generation, so making general assertions is tricky.

Mark

> Thank you,
> Lum
>
>
>     Lum Nforbi wrote:
>      > Hello all,
>      >
>      >     I have built a parameter file for the AOT surfactant molecule and
>      > tried to minimize the energy of a mixture of several of this molecule
>      > and water molecules but I have the warnings at the bottom part of
>     this
>      > mail. Gromacs basically goes through all the lines of parameters
>      > starting from [ bonds ] and says the parameters are too few. I am
>     also
>      > using the charmm force field.
>      >
>      >     Here is the way I constructed the aot.itp parameter file. I
>     am not
>      > sure this is correct. Excerpts of the parameter file are belowl.
>      >
>      > - I drew the AOT molecule and did the bond and angle connections
>     in the
>      > molecule.The atom names are provided by the ffcharmm27.atp file. All
>
>     The .atp file contains atom types, not atom names.  Your [bonds],
>     [angles], etc.
>       should be numbers, not atom types or names.  For instance, if
>     atoms 1 and 2
>     are bonded:
>
>     [ bonds ]
>     1    2    (function type, etc)
>
>      > values are obtained from the ffcharmmbon.itp file and
>     ffcharmmnb.itp file.
>      > - I am not sure how to build the dihedrals since the are X's in the [
>      > dihedrals ] section of the ffcharmmbon.itp file.
>      >
>
>     As Mark indicated earlier, an X is simply a wildcard - it can
>     correspond to any
>     number of atom types.
>
>      > My question is: Why does the program say I have few parameters
>     while I
>      > just out together parameters from the charmm27 force field?
>     Please, if I
>      > am doing something wrong, can someone let me know?
>      >   [ bonds ]
>      > ; i    j    func    b0    kb
>      > SL    O2L    1    0.1448    451872.0
>
>     You're using either atom types or names in these sections, which is
>     completely
>     incorrect.  Please have a thorough read through Chapter 5 of the manual.
>
>     <snip>
>
>      > NOTE 1 [file aotwater.top, line 19]:
>      >   System has non-zero total charge: -1.350000e+01
>      >
>
>     I would also be *very* concerned about this line.  You have a
>     negative charge of
>     -13.5, indicating that whatever charges you've assigned to your
>     small molecule
>     have left a fractional charge on the system, which is clearly
>     non-physical.
>
>     -Justin
>
>      > processing coordinates...
>      > double-checking input for internal consistency...
>      > renumbering atomtypes...
>      > converting bonded parameters...
>      > initialising group options...
>      > processing index file...
>      > Analysing residue names:
>      > Opening library file
>     /usr/local/gromacs/share/gromacs/top/aminoacids.dat
>      > There are:    60      OTHER residues
>      > There are:     0    PROTEIN residues
>      > There are:     0        DNA residues
>      > Analysing Other...
>      > Making dummy/rest group for T-Coupling containing 1110 elements
>      > Making dummy/rest group for Acceleration containing 1110 elements
>      > Making dummy/rest group for Freeze containing 1110 elements
>      > Making dummy/rest group for Energy Mon. containing 1110 elements
>      > Making dummy/rest group for VCM containing 1110 elements
>      > Number of degrees of freedom in T-Coupling group rest is 3192.00
>      > Making dummy/rest group for User1 containing 1110 elements
>      > Making dummy/rest group for User2 containing 1110 elements
>      > Making dummy/rest group for XTC containing 1110 elements
>      > Making dummy/rest group for Or. Res. Fit containing 1110 elements
>      > Making dummy/rest group for QMMM containing 1110 elements
>      > T-Coupling       has 1 element(s): rest
>      > Energy Mon.      has 1 element(s): rest
>      > Acceleration     has 1 element(s): rest
>      > Freeze           has 1 element(s): rest
>      > User1            has 1 element(s): rest
>      > User2            has 1 element(s): rest
>      > VCM              has 1 element(s): rest
>      > XTC              has 1 element(s): rest
>      > Or. Res. Fit     has 1 element(s): rest
>      > QMMM             has 1 element(s): rest
>      > Checking consistency between energy and charge groups...
>      >
>      > NOTE 2 [file aotwater_min.mdp, line unknown]:
>      >   You are using a plain Coulomb cut-off, which might produce
>     artifacts.
>      >   You might want to consider using PME electrostatics.
>      >
>      >
>      > This run will generate roughly 1 Mb of data
>      > writing run input file...
>      >
>      > There were 2 notes
>      >
>      > There were 142 warnings
>      >
>      > -------------------------------------------------------
>      > Program grompp, VERSION 4.0.5
>      > Source code file: gmx_fatal.c, line: 481
>      >
>      > Fatal error:
>      > Too many warnings (142), grompp terminated.
>      > If you are sure all warnings are harmless, use the -maxwarn option.
>      > -------------------------------------------------------
>      >
>      >
>      > I appreciate your answers.
>      >
>      > Lum
>      >
>
>     --
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>
>
>     ------------------------------
>
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>     End of gmx-users Digest, Vol 72, Issue 8
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