So you have to find or build residue templates and load them before loadpdb. Have you studied the tutorials yet? They are good for this. By now you should also have found papers by people who have done this in Amber to get the parameters at least.
Bill
<div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/24/2015 10:44 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
</div>No it cannot recognize the residues in the pdb file
On Monday, August 24, 2015 10:11 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Mon, Aug 24, 2015 at 1:28 PM, mohammad r <mohammad.r0325.yahoo.com>
wrote:
> I tried loadpdb, but it couldnot read it.
>
Is it a PDB file?? If loadPDB doesn't read it, there is probably
something wrong with the PDB file and it violates the PDB standard in some
way.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 24 2015 - 12:30:04 PDT
