You should look at the ATP topology and see if the parameters you are using
look sensible. Where did you get the topology from, did you use the united
atom one already in the GROMOS96 ff? Also did grompp give you any warnings
before your minimisation?
Tom
--On Thursday, August 16, 2007 01:04:55 +1000 Mark Abraham
<[EMAIL PROTECTED]> wrote:
[EMAIL PROTECTED] wrote:
Dear Mark:
Please keep correspondence on the list for others to see and use.
Thanks for your help about my problem of running GROMACS energy
minimization. I do what you suggestion, and the protein's minization
seems to be correct, it run about 300 steps and the Ep convergent
finally, but the ATP's minimization stopped at 14 stpes. So it means
the ATP's topology is broken? what is it means? What should I do?
So how do you think you would be able to tell whether either or both of
these chemical structures were in a sensible energy minimum? What
observables will be useful to you here?
Mark
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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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