Thank you so much f the recommendation, Prof!
Zalikha Ibrahim
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Zalikha Ibrahim <zalikha.ibrahim.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, July 17, 2012 8:02 PM
Subject: Re: [AMBER] Defining bonds between calcium and protein
On Tue, Jul 17, 2012, Zalikha Ibrahim wrote:
>
> I am new to Amber. I am using Amber8 and wanted to simulate a protein
> with 5 calcium ions as regulator.
I'd strongly recommend upgrading to a current version. Amber 8 was released
eight years ago, and the code and its force fields are quite out of date.
> > bond 1WD9.349.OE1 1WD9.900.Ca
> bond: Argument #2 is type String must be of type: [atom]
> usage: bond <atom1> <atom2> [order]
Use the "desc" command in LEaP to find atom and residue names in your unit.
LEaP numbers residues starting at 1, and it may have different numbers than
you think.
> 2) I couldnt find frcmod.ff99SB file (it may due to the use of Amber8,
> this is all I have). Can I just use ff99?
The current recommended protein force field is ff12SB. You need an update.
....dac
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Received on Tue Jul 17 2012 - 19:30:03 PDT
