[gmx-users] tfe

[Justin A. Lemkul]

shahrbanoo karbalaee wrote:
> Dear justin
>  for have  tfe30% after I got tfedrg.top with pdb2gmx and force field
> gromos965a.
> I do t this command :
> editconf -f tfedrg.gro -bt dodecahedron -d 0.71 -o box.gro
> genbox -cp box.gro -cs spc216.gro  ci tfedrg.gro - nmol 40  -p
> topol.top -o solvated.gro
>  I did that command with spc.gro(I rename spc216 to spc.gro) so.

I don't understand what you mean.  You show the use of spc216.gro...

> I got this  error:creating statusfile for 1 node...
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 165 of the 1596 non-bonded parameter combinations
> ERROR 0 [file "topol.top", line 57]:
>   No default Proper Dih. types

grompp is telling you where the error is.  What is on line 57?  What atoms are 
involved?  Are these parameters in the *bon.itp file for your force field?

> Excluding 1 bonded neighbours for TFE 18

I thought you tryed to insert 40 of these...you might want to check what went wrong.

> Excluding 2 bonded neighbours for SOL 5777
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #   G96BONDS:   108
> #  G96ANGLES:   144
> #      PDIHS:   36
> #       LJ14:   72
> #     SETTLE:   5777
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1182
> 
> Fatal error:
> There was 1 error in input file(s)
> 
> -------------------------------------------------------
> 
> the top file is attached.
> another question  please: if i use opls doI must have rtp file.  and
> add tfe. information  to this file?

This is not specific to OPLS.  If you want to use pdb2gmx to create your 
topology (under any force field), then yes, you need an .rtp file.  Otherwise, 
you make the topology by hand.

-Justin

> thank u for suggestion and help
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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