AMBER Archive (2009)

Subject: Re: Fw: [AMBER] Re: pls help and suggest

From: Gustavo Seabra (
Date: Fri Jul 17 2009 - 11:50:59 CDT

On Thu, Jul 9, 2009 at 2:45 PM, Vishal Maingi<> wrote:
> one more query is that if I ultimately make dendrimer by using GAFF
> parmetrised residues (less than 200 atoms in each residue so that I can use
> antechamber), then finally dendrimer will contain large number of atoms. after
> this I need to save prmtop inpcrd files for that I will again use GAFF (correct me
> if I am wrong). now my confusion is would it be nice to use GAFF for dendrimer
> which contains large number of atoms(as GAFF is good for small molecules)
> or else it wont matter if I have already used GAFF for small residues.

That's OK. You will use antechamber/GAFF to parameterize the small
units that make the dendrimer. I still think that the units should be
much smaller than 200 atoms, but I haven't seen your molecule, so I'm
not sure what happens in your case.

Then you will use LEaP to build the inpcrd/prmtop files using GAFF,
there's no problem here, it will be applied to the small parts
individually. You *may* have to enter parameters for the angles/bonds
that connect one residue to the other though. I hope someone with more
experience in this area can chime in here.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q:      Why do mountain climbers rope themselves together?
A:      To prevent the sensible ones from going home.

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