Re: [AMBER] parameters for anchor-modified glycopeptides

From: Urszula Uciechowska <urszula.uchiechowska.chem.umu.se>
Date: Mon, 7 Nov 2011 10:58:39 +0100

Dear Francois,

I was wondering, how did you prepare the ACE-LYA.pdb file in xleap?
when I load it by typing x = loadpdb ACE-LYA.pdb I get list of different errors...

Thank you for helping me
Urszula

________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Freitag, 4. November 2011 12:16
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides

Urszula,

> I am generating the files for my peptide using R.E.D and I was
> wondering how to correctly define those
> INTRA-MCC keyword? is there any manual for that? or could you give
> me some advise how to define it?

See the RESP manual for the definition of intra-molecular charge
constraint within the RESP inputs:
http://q4md-forcefieldtools.org/RED/resp/

The INTRA-MCC keyword in the P2N file format:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
  &
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/P2N/Central-frag-Pept/Mol_red1.p2n

regards, Francois



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Received on Mon Nov 07 2011 - 02:30:02 PST