[gmx-users] problem in generation of tpr file

[Mark Abraham]

On 24/01/2012 9:24 PM, Anushree Tripathi wrote:
> I have replaced all HW by H in ffnonbonded.itp.After executing the 
> command:
> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
> I am getting this error:
>
> File input/output error:
> dppc128.gro

This file likely does not exist. Use a file that exists.

>
> should I replace all HW with H (without delecting numbers that is 
> given in dppc128.pdb alongwith HW) in dppc128.pdb file?

Think first. grompp hasn't complained about the contents of this file, 
because it hasn't seen it. So don't make changes that aren't in the 
tutorial that aren't fixing the problem.

Mark

>
>
>
>
>
>
> On Mon, Jan 23, 2012 at 6:41 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Anushree Tripathi wrote:
>
>         I am going through the Justin Lemku tutorial for KALP15 in
>         DPPC.  I have
>         reached step three, when I try to generate a trp file for DPPC
>         only by
>         means of :
>
>         grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
>         I get the following warning:
>
>         Fatal error:
>         Atomtype OW not found
>
>         Any idea as to what causes this problem?
>
>
>     You constructed the force field incorrectly by deleting or
>     commenting out a line (or more) related to OW.  Re-check the
>     instructions provided in the tutorial.
>
>     -Justin
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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