AMBER Archive (2005)

Subject: RE: AMBER: How to build dynamics input for guanine with tleap ?

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Thu Feb 24 2005 - 08:35:23 CST

>
>1.How to build dynamics input for guanine with tleap ?
>

I think a good guide step-by-step to this question would be repeating some
AMBER tutorials on the web.

>When i try to make input form standard guanine pdb generated from HyperChem
>i get that error
>
> DG = loadpdb dg.pdb
>Loading PDB file: ./dg.pdb
> total atoms in file: 33
> Leap added 1 missing atom according to residue templates:
> 1 H / lone pairs
>

This is not an error, perhaps. Leap just adds any atoms which are missing.

>2.What method is used to calculation energy of solwatation ?

You can use several programs, the more popular being DelPhi, to solve
Poisson Boltzmann eqn. which can give you reliable electrostatic
contribution to the free energy of solvation...

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