> After I remove the water molecules, an average structure was calculated, but
> the output PDB file does not look right.
> pdb file:
>
> ATOM 1 HO1 ROH 1 ************************ 0.00 0.00
> ATOM 2 O1 ROH 1 ************************ 0.00 0.00
> ATOM 3 C1 4GA 2 ************************ 0.00 0.00
> ATOM 4 H1 4GA 2 ************************ 0.00 0.00
> ATOM 5 C2 4GA 2 ************************ 0.00 0.00
> ATOM 6 H2 4GA 2 ************************ 0.00 0.00
> ........
Yes indeed. The star/asterisk values mean that the precision on the
numbers was blown, i.e. each was larger than 9999.999 and suggests this is
more than an averaging issue since if the system was highly mobile, the
averages would tend to small values.
Likely you do not have wrapping turned on and therefore need to image the
trajectory. Then the molecule of interest has to be put into a common
reference frame via an RMS fit or some such. Without further information
on how you created your average structure, we cannot help...
--tec3.utah.edu
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Received on Tue Mar 22 2011 - 16:30:06 PDT
