AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
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:
http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0

PDB file format:
http://www.wwpdb.org/documentation/format23/v2.3.html

Using Tripos mol2 file format in LEaP:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15

regards, Francois

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber