Thank you Ilyas, now i am not sure what i did wrong. NMR restraint was 0
when i tried this simulation with solvent.
luckily i was able to get it to work without water which worked for me.
wrote:
> Taufik,
>
> I tested your system again, but now I solvated it with water. I followed
> the same minimization procotol. After 5000 steps, I see the NMR restraints
> still working (went down from 12 kcal/mol to 0.32 kcal/mol in this
> period). Looks like that nmropt=1 works fine.
>
> On Sat, 20 Dec 2008, Taufik Al-Sarraj wrote:
>
>
>> 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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>>
>>
>
>
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Received on Wed Dec 24 2008 - 01:12:21 PST
