I would never load the mol2 with modified residues but standard residue names. You could edit it to fix the residue names, keeping in mind that the name length is limited. Also when making templates, make sure you do isolated residues.
Charge definition is a significant effort, and reviewers may take a close look at what you do. The RED site may be useful; I haven't used it (or derived charges for that matter).
Bill
<div>-------- Original message --------</div><div>From: jacob wick <jacobwick.la.gmail.com> </div><div>Date:03/20/2015 8:09 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] loading molecule in xleap and saving it in mol2 format </div><div>
</div>I have loaded one pdb with standard residues and then deleted some of the
sugar bonds. Saving the modified file as mol2, this time also, without
changing the residues name I am getting the modified structure (visualizing
the structure using vmd). This file also has the partial charge column.
Is nucleic12.lib and loaded force fields like 14SB/bsc0 force fields are
capable of adding partial charges on modified residues also. Please suggest!
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Received on Fri Mar 20 2015 - 09:00:02 PDT
