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On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote:
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<div>Hi everyone!</div>
<div> </div>
<div>I was able to generate a pdb file in which the
hydrogens for the molecule are already included (that
way I avoided using the hdb file for the pdb2gmx).
However, when I checked the posre.itp, the some of the
restraints were applied to the hydrogens. Is this
correct because I am not sure since I what I know is
that the restraints should be applied to heavy atoms.</div>
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<br>
Maybe your atom names are confusing pdb2gmx. Maybe you're comparing
apples and oranges with the indices in the coordinate file and the
indices in the posres.itp (which are relative to the [atoms], IIRC).<br>
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<div>Are the positional restraints needed only for
the equalibration step but not for the production runs
in normal MD simulations. Thanks. </div>
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<br>
Up to you. Do you want to sample under unphysical restraints or not?<br>
<br>
Mark<br>
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