So, you mean I should derive the charge of the individual amine molecule and phenol molecule independently? After that using TER card at pdb for them individually too because they are not bonded?
________________________________
From: case <case.biomaps.rutgers.edu>
To: jun kit <klorin2002.yahoo.co.uk>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 10 November 2011, 11:15
Subject: Re: [AMBER] help with antechamber
On Wed, Nov 09, 2011, jun kit wrote:
>
> Warning: detected more than 10 Residue sequence numbers;Â this may be a
> large multiple residue PDB file;large multiple residue PDB files are not
> supported. Continuing, but problems may be encountered.
Oh my, you input pdb file has lots of problems. First, the waters at the
beginning should be removed: Amber has several built-in water molecules,
and you don't want to use antechamber to create a force field for water.
Second, for the LIG, take just *one* residue (of each chemical type) and
give it to antechamber; then load the library and frcmod files you get
into LEaP, finally using loadPdb to read in an edited version of your pdb
file. (Editing: make the water atoms and residues have proper names; put
a TER card between each individual molecule.)
...good luck....dac
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Received on Sun Nov 20 2011 - 13:00:03 PST
