Dear Daniel,
Thanks a lot for the suggestions, it is really helpful.
Actually, we also just figured it out and decided to use option (1)
to restart the simulations, from where the ligand was treated out.
All the best,
Qinghua
On 11/20/2017 04:59 PM, Daniel Roe wrote:
> Hi,
>
> Distance restraints in Amber are not imaged. So, if the ligand in your
> restart file has been imaged and the receptor has not, the distance
> restraints will not correct for that. The solution is to either 1)
> autoimage your restart files so that when you use them as input
> coordinates the imaging artifact is gone or 2) run with iwrap=0 and
> use NetCDF trajectories/restarts.
>
> Hope this helps,
>
> -Dan
>
> On Sun, Nov 19, 2017 at 9:58 AM, Qinghua Liao <scorpio.liao.gmail.com> wrote:
>> Hello All,
>>
>> Some additional information regarding to my previous post, here is the
>> input file I used for the production runs:
>>
>> MD simulation
>> &cntrl
>> imin = 0, nstlim = 25000000 , irest = 1, ntx = 5, dt = 0.002 ,
>> ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
>> ntc = 2, ntf = 2, cut = 10.0 , ntwprt=7586 ,
>> ntb = 2, ntp = 1, pres0 = 1.0, taup = 1.0, barostat=2,
>> ioutfm = 1, iwrap = 1, nmropt=1,
>> ntwx = 5000, ntpr = 5000, ntwr = 50000 ,
>> /
>> &ewald
>> /
>> &wt type = 'END'
>> /
>> &rst
>> iat=130,7570, r1=1.0, r2=1.5, r3=3.2, r4=3.8,
>> rk2=5.0, rk3=5.0,
>> /
>> .
>> . some more distance restraints
>> .
>>
>>
>> I suspect that Amber does not write out the restart file properly, or
>> the restart runs were not dealt with properly. Could some one please
>> have a check for me? It really bothers me. Thanks a lot!
>>
>>
>> All the best,
>> Qinghua
>>
>>
>> -------- Forwarded Message --------
>> Subject: simulations of enzyme with ligand
>> Date: Thu, 16 Nov 2017 17:51:19 +0100
>> From: Qinghua Liao <scorpio.liao.gmail.com>
>> To: AMBER Mailing List <amber.ambermd.org>
>>
>>
>>
>> Hello,
>>
>> I did some simulations of an enzyme in complex with a ligand, the
>> complex sits in a octahedral box with water molecules.
>> I applied some distance restraints between the ligand and the enzyme in
>> order to keep the ligand stable at the binding site,
>> the force constant was set as 5 kcal/mol A2.
>>
>> However, I found that there are some snapshots that the ligand goes out
>> of the binding site. I thought that it could be
>> the PBC problem, but I still got the long distance between the ligand
>> and the enzyme after I did the correction with autoimage.
>> I then check the output file, I found the restraints energy was
>> extremely high than the other frames.
>>
>>
>> Here are the distances calculated using cpptraj with autoimage
>> correction (only one of four is present):
>> # frames distance (angstrom)
>> 14999 3.1086
>> 15000 2.8088
>> 15001 52.0178
>> 15002 14.3344
>> 15003 3.4264
>> 15004 3.0565
>>
>> And here are the restraints from the output file:
>> # frames Restraints (kcal/mol)
>> 14999 0.0350
>> 15000 0.4185
>> 15001 1209.4373
>> 15002 294.3320
>> 15003 20.4252
>> 15004 20.2892
>>
>> As I did the production runs step by step, each step is for 50 ns (5000
>> frames). It means that the jumping-out happened
>> at the first frame of step 4 (frame 15001). I then checked the last
>> frame of step 3 ( frame 15000) from the restart file,
>> I found that the ligand was out of the binding site, and the restart
>> file which was not done with PBC correction (the ligand is still out of the
>> enzyme) was used for the the next step simulation. I did the simulations
>> with iwrap=1 and ioutfm=1.
>>
>> Any comment and suggestion? Thanks a lot!
>>
>>
>>
>> All the best,
>> Qinghua
>>
>>
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>
>
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Received on Mon Nov 20 2017 - 08:30:03 PST
