> I hve run a 1.5ns simulation on a 12 mer DNA in explicit solvent with
> PBC. i wanted to calculate the average structure without (excluding)
> solvent and ions. the following is the input i gave to ptraj. I am
> getting the structure but it is highly scattered and not a proper one.
>
> trajin mde.mdcrd
> trajin mdp1.mdcrd
> trajin mdp2.mdcrd
> average avgst.pdb pdb nowrap
> center :1-24
> image familiar
> strip :WAT
> strip :Na+
As pointed out by the other post on the reflector, the commands to ptraj
are order dependent. You want to create the average structure AFTER you
image (and likely RMS fit to a common reference frame). During imaging,
molecules can separate, so you may want to image the first strand first,
then image again...
center :1-12 mass origin
image origin center
center :1-24 mass origin
image origin center familiar
rms first mass out rms.dat :1-24
strip :25-999999
average avgst.pdb pdb nowrap
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Received on Mon Nov 21 2005 - 16:53:02 PST
