Dan,
Many thanks. Sorry for the ambiguity of my message. Indeed, I used the average files.
All the best
George
On Aug 22, 2011, at 6:08 PM, Daniel Roe wrote:
> Hi,
>
> Are you talking about the "test-out.rep.cX" files, "test-out.c*"
> files, or "test-out.avg.c*" files? If you are talking about the
> "test-out.avg.c*" files this behavior is not unexpected since you are
> averaging over the coordinates of all structures within that cluster.
> In my opinion the average structure isn't really that useful (I never
> use the average keyword), since it does tend to be distorted. I think
> it's better to just calculate whatever property you're looking for (a
> distance, RMS, etc) on the entire cluster ("test.out.c*") and average
> that.
>
> Also, why are you centering and imaging your coordinates at all? Since
> the cluster command you are using uses best-fit RMSD as a metric it
> doesn't matter where your coordinates start from. Just do the
> clustering and forget about imaging and centering - it won't change
> the results and will be faster.
>
> Hope this is helpful.
>
> -Dan
>
> On Sat, Aug 20, 2011 at 7:08 AM, George Tzotzos <gtzotzos.me.com> wrote:
>> Hi everybody,
>>
>> I'm trying to cluster the trajectory frames of a 2ns production run of a solvated complex (138 residues).
>>
>> Using ptrja my.prmtop cluster.in
>>
>> where cluster.in is
>>
>> trajin prod_2ns.mdcrd
>> center :1-138 mass origin
>> image origin center familiar
>> cluster out test-out representative pdb \
>> average pdb averagelinkage clusters 5.0 mass rms :1-138 .CA
>>
>> produces clusters. However, when I try to visualise the clusters some frames show with unrealistic bond lengths.
>>
>> I believe the problems is in the centering and imaging.
>>
>> I'd appreciate if anyone could help to correct the above script.
>>
>> Thanks in advance
>>
>> George
>>
>>
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Received on Mon Aug 22 2011 - 11:00:03 PDT
