Hello Abhishek,
Thanks very much for your suggestion. I tried, but it did not work for me.
All the best,
Qinghua
On 01/25/2017 05:37 PM, Thakur, Abhishek wrote:
> Hi Liao,
>
>
> You can try, I have made some small minor changes in your script
>
>
>>>> &wt type='DUMPFREQ', istep1=50, /
>>>> &wt type='END', /
>>>> DISANG=restraints.dat
>>>> DUMPAVE=distance.dat
>>>>
>>>> cat > restraints.dat << EOF
>>>> Harmonic restraints for distance of 1.6 angstrom
>>>> &rst
>>>> iat=345,425,
>>>> r1=0, r2= 1.6, r3= 1.6, r4=5.0,
>>>> rk2= 500.0 , rk3= 500.0 ,
> /
> EOF
>
>
> With regards,
> -AT
>
>
> ________________________________
> From: Qinghua Liao <scorpio.liao.gmail.com>
> Sent: Wednesday, January 25, 2017 5:15:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] distance restraints failed
>
> Hello Hai,
>
> Thanks for your tips. Actually, I am following the same protocol for a
> similar system from a paper.
> They also used a distance of 1.6 for the starting window. :-
>
> All the best,
> Qinghua
>
> On 01/25/2017 04:52 PM, Nhai wrote:
>> 1.6 A is very close to bond length.
>>
>> Hai
>>
>>
>>
>> Hai Nguyen
>>> On Jan 25, 2017, at 10:49 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>>>
>>> what does your MD output say about the restraints? It should tell you if it
>>> read them, and also the energies will tell you how much restraint strain
>>> you have.
>>>
>>> On Wed, Jan 25, 2017 at 10:44 AM, Qinghua Liao <scorpio.liao.gmail.com>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am doing umbrella sampling with amber16, the reaction coordinates are
>>>> the distances
>>>> between a metal ion and an oxygen of a water molecule. But I found that
>>>> the distance restraints
>>>> were failed for some windows. Here are my input files:
>>>>
>>>> &cntrl
>>>> imin = 0, nstlim = 25000, irest = 0, ntx = 1, dt = 0.002 ,
>>>> ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
>>>> ntp = 1, pres0 = 1.0, taup = 2.0,
>>>> ntb = 2, cut = 12.0 ,
>>>> ntc = 2, ntf = 1,
>>>> iwrap = 1, nmropt = 1 ,
>>>> ntwe = 5000, ntwx = 5000, ntpr = 5000, ntwr = 5000,
>>>> /
>>>> &wt
>>>> type='DUMPFREQ', istep1=50, /
>>>> &wt
>>>> type='END',
>>>> &end
>>>> DISANG=restraints.dat
>>>> DUMPAVE=distance.dat
>>>>
>>>>
>>>> Harmonic restraints for distance of 1.6 angstrom
>>>> &rst
>>>> iat=345,425,
>>>> r1=0, r2= 1.6, r3= 1.6, r4=5.0,
>>>> rk2= 500.0 , rk3= 500.0 ,
>>>> &end
>>>>
>>>> What I got for the distances from the simulation are around 2.0
>>>> angstrom, it never approaches 1.6 angstrom.
>>>> I even tried with a much higher force constant like 1000 kcal/mol A2,
>>>> then the distances go to around 1.9 angstrom,
>>>> but still not 1.6. However, the restraints are working for those windows
>>>> with restrained distances more than 2 angstrom.
>>>>
>>>> Then I also try to restrain a distance between two water molecules at a
>>>> distance of 1.6, the restraints was also failed.
>>>> Similarly, it worked if I want to restrain the distance at 3.0 angstrom.
>>>>
>>>> This is strange to me. Though we may think that the interaction between
>>>> a water molecule and the metal ion could be very
>>>> strong, a force constant of 500 or even 1000 kcal/mol A2 should make it
>>>> work. Could someone help me out of the problem?
>>>> Any response will be highly appreciated!
>>>>
>>>>
>>>> All the best,
>>>> Qinghua
>>>>
>>>>
>>>>
>>>>
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Received on Wed Jan 25 2017 - 11:30:03 PST
