AMBER Archive (2007)

Subject: Re: AMBER: Charge not integral. Head-to-tail cyclic peptides

From: Laurent Chiche (chiche_at_cbs.cnrs.fr)
Date: Mon Jun 18 2007 - 09:37:53 CDT

Giacomo Bastianelli wrote:
> Dear Amber users,
>
> I run Amber 9.0 on a Linux OS and I have been trying to
> run molecular dynamics on head-to-tail cyclic peptides.
> I have problems to balance the total charge of the protein.
>
> ERROR: The unperturbed charge of the unit: -1.594100 is not integral.

Hello,
The way you built MCoTI-II is not correct.
Run tleap then
> ClearPdbResMap
> myprot = LoadPdb myprot.pdb
> Bond myprot.1.N myprot.34.C
> check myprot
> SolvateOct myprot TIP3PBOX 10
> SaveAmberParm myprot myprot.top myprot.crd

The ClearPdbResMap avoids replacing the first and last residues by
by standard terminii (NH3+, COO-)
Also note that it is not necessary to add ions since a neutralizing plasma
will be used if you use PME.

Hope this helps
Laurent 

-- 
-----------------------------------------
Dr Laurent Chiche
Directeur de Recherche au CNRS
Centre de Biochimie Structurale
CNRS UMR 5048 - UM 1 - INSERM UMR 554
29 rue de Navacelles
34090 MONTPELLIER Cedex  - France

Tel: (33)[0]4 67 41 77 03
Fax: (33)[0]4 67 41 79 13
Email: chiche_at_cbs.cnrs.fr
Web: http://www.cbs.cnrs.fr
      http://knottin.cbs.cnrs.fr
-----------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu