I used KALP-15 in DPPC, GROMACS version 4.5.3 to check the stability of my membrane lipid. In step 2 ( Define box and solvent) when we are trying to pack the lipids around the protein, they have asked to perform energy minimization but unfortunately "confout.gro" is not generated, so we need your guideline how to generate this file.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein_old/03_solvate.html
confout.gro is the output of energy minimization. If you don't have it, either EM failed (which should have been accompanied by obvious messages) or it is named something different. As I mention in the tutorial, "confout.gro" simply refers to this output, in case you have named it something else.
Thank you sir for positive response, but we are facing difficulty in performing energy minimization using -mdrun, can please elaborate the command to be used .
If you named the .tpr file produced by grompp "em.tpr" it is simply:
mdrun -s em.tpr
Substitute whatever file name you might have used.
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