I am quite new to this, how to create a library for this?
Could please help me,
Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 1. November 2011 15:11
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides
Urszula,
> My problem is that AMBER is not handling that ( ff99SB), there is
> not sugar unit right now,
>
> when I am loading f.ex pep1.pdb to the tleap i am getting:
>
> Checking 'x'....
> WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
-> A warning not a big deal ;-)
> FATAL: Atom .R<CLYS 12>.A<HC 24> does not have a type.
Yes this is the open valency I told you; LEaP reports a CLYS
residue... that has an aldehyde function instead of a carboxylate one;
you simply need to modify the C-terminal residue according to the FF
lib you are going to load in LEaP; in your case I guess you want to
use CLYS... or you need to create a new FF library for this
alpha-amino-...aldehyde ;-)
regards, Francois
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Received on Tue Nov 01 2011 - 08:00:09 PDT
