AMBER Archive (2007)

Subject: AMBER: CRESP charges in antechamber prepin

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Aug 20 2007 - 02:23:24 CDT

I am replacing AM1-calculated charges in antechamber prepin with CRESP charges
(calculated HF/6-31G* by formally cutting the 98-atoms charge = 0 molecule,
into two residues). I see so large trend differences, that I want to compare
QM-MM for the two types of charges, before embarking in thermodynamic
integrations (and hopefully dftb, if I get the needed files).

QUESTION 1: CRESP charges are calculated at double precision, i.e. are given at
6 decimals. I expect that rounding off to the 5 decimals of prepin may led to
unbalance. If so, is any way out (particularly for other molecules in my list
of interests which bear a net charge)?

QUESTION 2: I also wonder whether I am taking a longer route than needed:
because antechamber changes atom numbering, I preliminarily obtained prmtop and
inpcrd files with the original antechamber prepin in order to find through VMD
the correspondence of atom numbering antechamber/CRESP. Then, manually, I am
replacing antechamber charges with CRESP charges in prepin file, getting a new
prepin file. Finally, I'll recalculate prmtop and inpcrd with the new prepin
file (and solvation, this time). Is any less time consuming alternative?

Thanks
francesco pietra

       
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