Hey,
could you keep me informed about your conclusions on these problems you
have? I have to cope with the exact same problem and would highly
appreciate if I could get any impact on that.
Thanks a lot!
AnnA
Am 10.10.2012 14:24, schrieb Jitesh Doshi:
> Hi David,
> Thanks a lot.
>
> Yes.. The problem is there..the starting energy in step 0 of md is much
> higher .. and nowhere near the energy in last step of minimization. How
> should I look into the matter?
> Yes i do have one non-standard residue.. my ligand..
> Also when i visualized the structures after minimization, and what i
> observed is the liagnd molecule loses its original connectivity. And the
> new ligand in minimized structure is distorted and broken. Why this could
> be happening?
> I'll check the smaller MD run and visualize the trajectory.
> On Wed, Oct 10, 2012 at 4:46 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Wed, Oct 10, 2012, Jitesh Doshi wrote:
>>
>>> I am running minimization in three steps, with PBC on,
>>> 1. all atoms restrained
>>> 2. only protein backbone atoms restrained
>>> 3. all atoms free
>>>
>>> all with 2500 steepest descent and 5000 conjugate gradient steps.
>>>
>>> and then moving to run heating and equilibration with following input
>> Make sure the energy at step 0 of the dynamics matches the last step of
>> minimization. Make sure that checkoverlap (in ptraj) reports no bad
>> contacts.
>>
>> Run a short (serial) simulation with ntpr=1, ntwx=1, nstlim=100. Visualize
>> your trajectory and look for suspicious behavior.
>>
>> You have a big system, and this may not be easy. If there is any
>> non-standard
>> part of your setup (not just ordinary amino acids...) look in that region
>> first.
>>
>> ...dac
>>
>>
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>
>
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Received on Thu Oct 11 2012 - 02:00:03 PDT
