AMBER Archive (2007)

Subject: Re: AMBER: problems visualizing mdcrd in VMD

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Oct 31 2007 - 05:33:37 CST

Mattia,

You need to use "crdbox" as file type ...

vlad

Mattia Mori - CERM wrote:

> Dear all,
> when I try to visualize trajectory in VMD programs I got great results
> only when I impose in my sander input file ntb=0.
> When I use ntb=2 and I load prmtop and mdcrd in VMD, I get a disaster
> and it's not possible to recognize any molecule in the animation,
> every bond is stretched to several amstrong.
> How can I visualize trajectory when I impose ntb=2?
> There are others useful visualization programs?
>
> Thanks in advance for your help.
>
> Mattia Mori
>
>--
>
>
>
>
>
>
>**-**-**-**-**-**-**-**-**-**-**-**-**
>
>Mattia Mori, PhD Student
>CERM - Centro di Risonanze Magnetiche
>via L. Sacconi 6,,
>50019 Sesto Fiorentino, FI
>fax (+39) 055 4573914
>tel (+39) 055 4573912
>www.cerm.unifi.it
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To
> unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu