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 - 06:41:42 CST

Mattia,

Changing the extension of the file will not help ....

When you load the molecule from the GUI, you need to choose the type
"AMBER Coordinates with periodic box"

If you load via a tcl script, the commands should be (you may have any
file extensions as you wish):

"mol new [file].parm type parm7 "
"mol addfile [file].mdcrd type crdbox"

assuming you are using AMBER7 or later (if you are using AMBER6 the
fitst command should be "mol new [file].parm type parm")

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
>
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-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
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Fax: ++49-6221-533298

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

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

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