[gmx-users] Incorrect number of atomtypes for dihedral

[Justin Lemkul]

On 7/20/12 2:00 PM, Debashis Sahu wrote:
> Dear all
>
>            I used Gromacs 4.5 for thio-Urea molecule  in OPLS-AA force
> field, but in grompp step I got an error as follows:
>
>
>
> ---------------------------------------------------------------------------------------
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
>
> checking input for internal consistency...
>
> processing topology...
>
>
>
> ERROR 1 [file ffbonded.itp, line 2634]:
>
>    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
>
>
>
>
>
> ERROR 2 [file ffbonded.itp, line 2636]:
>
>    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
>
>
>
> Generated 332520 of the 332520 non-bonded parameter combinations
>
> Generating 1-4 interactions: fudge = 0.5
>
> Generated 332520 of the 332520 1-4 parameter combinations
>
> Excluding 3 bonded neighbours molecule type 'Other_chain_X'
>
>
>
> NOTE 1 [file topol.top, line 94]:
>
>    System has non-zero total charge: -1.000000
>
>    Total charge should normally be an integer. See
>
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>
>    for discussion on how close it should be to an integer.
>
>
>
>
>
>
>
> processing coordinates...
>
> double-checking input for internal consistency...
>
>
>
> There was 1 note
>
>
>
> -------------------------------------------------------
>
> Program grompp, VERSION 4.5.5
>
> Source code file: grompp.c, line: 1372
>
>
>
> Fatal error:
>
> There were 2 errors in input file(s)
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> -------------------------------------------------------
> I tried lot of times to change the atom type mention in dihedral but failed.
>
> Can any one help me to recover this?
>
>

We'll need to see the problematic lines from ffbonded.itp along with what you 
have attempted.  Otherwise, there's no point in guessing.

-Justin

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

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

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