AMBER Archive (2003)

Subject: Re: AMBER: about some of the cards in Sander 7

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Wed Nov 12 2003 - 14:38:39 CST

Hi!
ntx=7 is there...just the manual lacks it.
the others I dont know ..maybe others will answer,
hope this helps,
vlaf

Pingna Xu wrote:

>Hi,
>
>I want to run molecular dynamics for protein-DNA system using Sander in Amber7.I have noticed that in Sander7,there are only options 1-6 for the card "NTX".But I want to set NTX=7 for the MD.Is that OK?
>And I also found that in Sander7,there is no "npscal" or "ndfmin" anymore.But the guys in our lab always set ndfmin=6 and npscal=1 for the MD since they use earlier versions of Amber.What should I do with these two cards since I am using Amber7?Thanks!
>
>Pingna
>
>
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-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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