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 <jalem...@vt.edu <mailto:jalem...@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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