Hello Changqing,
What do you mean by "different structures formed by ambpdb script from
last trajectory"? Do you mean when you run dynamics simulations, the
structures in the last frames of the trajectories are different, or do you
mean the structures produced right after the minimization step are
different? And how different are they?
Jane
On Tue, Feb 19, 2013 at 11:42 PM, Changqing Yan <ycqchemical.gmail.com>wrote:
> Dear,
>
> Happy Chinese New Year !
>
> Lately I encountered a problem. When I run the same job on different
> platform (that also means the version of amber is different, i.e. amber 9
> and amber 11 ), it seems that the results are different, which can be
> proved by different structures formed by ambpdb script from
> last trajectory (structures attached).
>
> BTW, my minimization input is:
>
> Initial minimisation of protein side chains and ions
> &cntrl
> imin=1, maxcyc=4000,ncyc=2000,
> cut=12, ntb=0, igb=1, ntr=1,
> /
> Hold Res 1-1466 protein backbone constrained
> 10.0
> FIND
> CA * * *
> SEARCH
> RES 1 1466
> END
> Go on
> 10.0
> FIND
> C * * *
> SEARCH
> RES 1 1466
> END
> Go on
> 10.0
> FIND
> N * * *
> SEARCH
> RES 1 1466
> END
> END
>
> Thx and regards,
> C.Q.Yan
>
> p.s. Structures are provided upon request (it is said they are too large to
> be accepted by the post system).
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Received on Wed Feb 20 2013 - 12:00:02 PST
