starting structure for docking



Dear CCLers,
 I hope you will bear with this question of mine but I wasn't able to agree with
 my colleague about it. I've docking a molecule, citrulline, to a protein and I
 obtained the citrulline molecule from a protein-citrulline complex from the PDB
 database website. I think it's suitable by just extracting the citrulline
 sequence and adding hydrogen to it and minimized the structure later on before I
 start my docking process.
 My colleague, however, doesn't think it's an appropriate way of getting a
 starting structure for docking and I should use a structure from a molecule
 database (i.e. the cambridge crystallographic database or etc). He says that
 maybe the starting structure I have used may not be correct in terms of bond
 lengths/angle or the torsions. I don't think that is the case, since I minimized
 the structure anyway, so it wouldn't be any major difference if i take it from a
 complex structure or if I build the structure from scratch (like using the
 Biopolymer module from InsightII) or if I obtained it as a single molecule from
 a database.
 I'm do apologize if this sounds very trivial but I would be grateful for some
 clarification as I know most of you will have experience in such matters.
 Thank you for your time.
 Rowyna K.
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