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

[Justin A. Lemkul]

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
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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