On 23/04/10 13:16, shahid nayeem wrote:
Dear All
I am trying to study inter peptide interaction fpr which I need to put
more than one peptide in one simulation box. I did it with genconf
command but this inserts peptide in a regular ordered manner I want
these to be in irregular disordered insertion. Even after using genconf
Well that's a difficult and atypical scenario. genconf -shuffle will
allow you to stack the same peptide in a regular array with random
rotations of the whole box. Then you can solvate, equilibrate and run MD
at a high temperature to give yourself a quasi-disordered starting state.
, I tried to proceed furthe after solvation with spc water. The energy
minimization (steepest descent) failed to converge even after 5000 steps
and theirafter position restraint dynamics failed giving segmentation
fault. Introducing more peptide after generating .gro with -ci -nmol
gives error showing more than one residue in insert molecule.
Please help me and write commands which I should follow.
No, because that's an impossible task. We can't begin to guess the
reasons for things failing without seeing the actual output (was the EM
energy large and negative? what was the actual error message from -ci
-nmol?).
You should be careful to start with a small test case so that you can
learn the workflow with a manageable problem. Can you get a single
peptide to equilibrate? Two stacked peptides? It is best to learn to
walk before trying to run :-)
Mark
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