[gmx-users] TFE Proper Dihedral types...

[Justin A. Lemkul]

On 5/15/12 12:14 PM, rama david wrote:
> Hi Gromacs Friends ..
>
> I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study..
> I am using G96 53a6 ff
>
> After the genbox -cp .. -cs tef.pdb -o mix.pdb
>
> I count the no of solvent molecule , to update
> topology ..
>
> after Grompp I am facing following error
> grompp -f minim.mdp -c mix.pdb -o em.tpr -p final.top
>
>
> ERROR 1 [file topol-tef.itp, line 46]:
>    No default Proper Dih. types
>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 3 bonded neighbours molecule type 'SOL'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 1372
>
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> I checked the topology for TFE, Dihedral section is as follow ...
>
>
> *
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1
> c2            c3            c4            c5
>      1     2     3     4     1    gd_24
>      2     3     4     5     1 *
>
>
>
>   So what to resolve the problem ..
>   All suggestions are welcome...
>

The parameters are missing from ffbonded.itp, making the implementation 
incomplete.  You can obtain a TFE topology from ATB:

http://compbio.biosci.uq.edu.au/atb/download.py?molid=1655

-Justin

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

Justin A. Lemkul, Ph.D.
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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