AMBER Archive (2005)

Subject: AMBER: Making prepin file for individual residues of huge molecule.

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Mon Mar 21 2005 - 09:00:11 CST

Dear amber-user,

I'm trying to make **.prepin file for individual residues of huge
molecule (dendrimer; atom number > ~5,000). Since antechamber cannot
cover such a huge molecule, I'll make prepin files of individual
residues, and then generate topology file of the molecule by using
leap. Coordinates were generated by INSIGHTII.
I'm having problem with making prepin file for individual incomplete
residues. For example, one of residue is "CH2CH2NH3+". Since this
residue has 26 electrons, which is even number, I cannot use "-nc 1"
option with antechamber. I can add H atom to make "CH3CH2NH3+", which
has odd numbers and can allow to use "-nc 1", but I don't think it is
good idea because this residue is a part of big molecule like
"-----CH2CH2NH3+". Same thing also happened to opposite situation like
having odd electron numbers for non-charged residue.
Could you tell me how to effectively generate prepin files (with
appropriate partial charges) in this situation, which is about making
prepin for incomplete residue of big molecule?

Thanks for your help in advance.

best,
Hwankyu.

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