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

From: Vineet Pande <>
Date: Thu, 24 Feb 2005 14:35:23 +0000

>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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Received on Thu Feb 24 2005 - 14:53:01 PST
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