AMBER Archive (2009)

Subject: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ?

From: FyD (
Date: Tue Mar 03 2009 - 08:12:18 CST

> On Tue, Mar 03, 2009, ?????? wrote:
>> I still have some questions.
> I suspect that you could answer most of these questions yourself, just
> by running some experiments. Try things out and see what happens!
> Running LEaP with bad input will *not* break your computer....
>> You answered that after loading mol2 file which contains
>> information about the charge I calculated, I should load pdb file.
>> Does this mean mol2 file is just used for the charge?
> The mol2 file has lots of information, charges, atom types,
> connectivity, and coordinates. You can use the coordinates that are
> there, or use the loadpdb command to load new coordinates into your
> structure.

Besides, you could read the following web site:

Tripos mol2 file format:,SimplePage,,,&page=sup_mol2&s=0

PDB file format:

Using Tripos mol2 file format in LEaP:

regards, Francois

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