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...

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu