On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote:
Hi everyone!
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.
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).
Are the positional restraints needed only for the equalibration step
but not for the production runs in normal MD simulations. Thanks.
Up to you. Do you want to sample under unphysical restraints or not?
Mark
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