[gmx-users] using the Fourier function for dihedral in the OPLS FF

[Justin Lemkul]

On 6/2/17 7:31 PM, Saeed Nasiri wrote:
> Dear Justin
> 
> I really thanks for your useful help in the last  topic.
> I totally changed the method. I copy the oplsaa.ff file in the working
> directory
> and insert the parameters in the related files.
> But I have a problem with dihedral parameters. As far as I know, the opls
> force filed used
> the Ryckaert-Bell function for dihedral. I used a set of parameters from a
> paper in which
> used the Fourier function. I insert the parameter of the Fourier function in
> the ffbonded.itp file:
> 
> 
> ;dihedraltypes

You're not using correct syntax.  You need [ dihedraltypes ] here.  Without it, 
nothing is interpreted correctly, so you get a cascade of errors.  Looks like 
you might have more typos or directives out of order based on what grompp is saying.

-Justin

> ;  i    j    k    l   func     coefficients
>    HCC    CTT    CSS    HCC     5      0.00000   0.00000   1.33050   0.00000
>    HCC    CSS    C22    HCC     5      0.00000   0.00000   1.33050   0.00000
>    HCC    C22    C11    H11     5      0.00000   0.00000   1.33050   0.00000
> 
>    CTT    CSS    C22    HCC     5      0.00000   0.00000   1.53130   0.00000
>    CSS    C22    C11    H11     5      0.00000   0.00000   1.53130   0.00000
>    C11    C22    CSS    HCC     5      0.00000   0.00000   1.53130   0.00000
>    C22    CSS    CTT    HCC     5      0.00000   0.00000   1.53130   0.00000
>    CTT    CSS    C22    C11     5      7.28000  -0.65690   1.16730
> 0.00000
> 
>    CWW    NAA    CRR    NAA     5      0.00000  19.46000   0.00000
> 0.00000
>    CWW    NAA    CRR    HCR     5      0.00000  19.46000   0.00000
> 0.00000
>    C11    NAA    CRR    NAA     5      0.00000  19.46000   0.00000
> 0.00000
>    C11    NAA    CRR    HCR     5      0.00000  19.46000   0.00000
> 0.00000
>    CRR    NAA    CWW    CWW     5      0.00000  12.55000   0.00000
> 0.00000
>    CRR    NAA    CWW    HCW     5      0.00000  12.55000   0.00000
> 0.00000
>    C11    NAA    CWW    CWW     5      0.00000  12.55000   0.00000
> 0.00000
>    C11    NAA    CWW    HCW     5      0.00000  12.55000   0.00000
> 0.00000
>    NAA    CWW    CWW    NAA     5      0.00000  44.98000   0.00000
> 0.00000
>    NAA    CWW    CWW    HCW     5      0.00000  44.98000   0.00000
> 0.00000
>    HCW    CWW    CWW    HCW     5      0.00000  44.98000   0.00000
> 0.00000
>    CWW    NAA    C11    H11     5      0.00000   0.00000   0.51900
> 0.00000
>    CRR    NAA    C11    H11     5      0.00000   0.00000   0.00000
> 0.00000
>    CWW    NAA    C11    C22     5     -7.15350   6.10640   0.79390
> 0.00000
>    CRR    NAA    C11    C22     5     -5.26910   0.00000   0.00000
> 0.00000
>    NAA    C11    C22    CSS     5     -7.47970   3.16420  -1.20260
> 0.00000
>    NAA    C11    C22    HCC     5      0.00000   0.00000   0.36700   0.00000
> 
> but the grompp command gives the following errors:
> 
> 
> ....
> ERROR 63 [file topol.top, line 255]:
>    No default Ryckaert-Bell. types
> 
> 
> ERROR 64 [file topol.top, line 256]:
>    No default Ryckaert-Bell. types
> 
> 
> ERROR 65 [file topol.top, line 257]:
>    No default Ryckaert-Bell. types
> 
> Excluding 3 bonded neighbours molecule type 'IL_cat_chain_A'
> 
> ERROR 66 [file topol.top, line 270]:
>    ERROR: The cut-off length is longer than half the shortest box vector or
>    longer than the smallest box diagonal element. Increase the box size or
>    decrease rlist.
> 
> 
> Removing all charge groups because cutoff-scheme=Verlet
> 
> There was 1 note
> -------------------------------------------------------
> 
> 
> after that I insert the dihedrals in a file (dihedral.itp) and included in
> the topol.top file
> but the following errors have printed out:
> 
> 
> 
> ....
> ERROR 4 [file topol.top, line 224]:
>    No default Fourier Dih. types
> 
> 
> ERROR 5 [file dihedral.itp, line 1]:
>    Invalid directive dihedral
> 
> 
> WARNING 1 [file dihedral.itp, line 6]:
>    Too few parameters on line (source file
>    /home/nasiri/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 1790)
> 
> 
> WARNING 2 [file dihedral.itp, line 7]:
>    Too few parameters on line (source file
>    /home/nasiri/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 1790)
> ....
> 
> 
> 
> 
> please tell me how to solve this problem.
> 
> thanks in advance for your help.
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================