AMBER Archive (2008)

Subject: Re: AMBER: distance restraint between non-bonded molecules]

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Sat Dec 20 2008 - 12:44:43 CST

That is what i noticed also, I am relieved. thank you Ilyas.
My simulation did not work when i used ntb=1 and solvated the system
with water.
but when i used ntb=0 and eedmeth = 5. The restraint in the simulation
worked
same as the tutorial
http://www.uni-koeln.de/themen/Chemie/software/amber7/tutorial/dna_NMR/nmr_dna_tutorial.htm

Thank you again for all your help,
Taufik

Ilyas Yildirim wrote:
> Taufik,
>
> I tried a couple tests on your structure, and whether I use a group of
> atoms or single atom to define at1 or at2, everything works fine. Did you
> try to re-install amber and see if that will solve the problem? If not, I
> will send you all the tests I've done. I am using amber9 by the way.
>
> On Fri, 19 Dec 2008, Taufik Al-Sarraj wrote:
>
>
>> Potentially dangerous attachments were identified and removed from this
>> message.
>>
>> of course,
>>
>> RSTdel is the original RST file and RST4 is the one i modified manually
>> to have the correct atom number.
>>
>> Best,
>> Taufik
>>
>>
>
>

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