Re: Bad structure after converting the coarse grained last frame to all-atom

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Sep 20 2018 - 11:14:35 CDT

At this point the best I can think is that you ought to post your structure
and precise command used for CG reversal, so folks here can have a look.
Best,
Peter

On Thu, Sep 20, 2018 at 10:58 AM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> The minimization shows a lot of warning like-
>
> Warning: Bad global bond count! (74224 vs 74704)
> Warning: Bad global angle count! (88963 vs 91517)
> Warning: Bad global dihedral count! (96371 vs 102836)
> Warning: Low global exclusion count! (251495 vs 268840)
>
> Warning: Tuple 38411 with atoms 14385(180) 14384(180) 14396(184)
> 14398(184) missing patch 184
>
> And the stretching does not remove even affter minimization.
>
> Rabeta Yeasmin
>
>
> On Wed, Sep 19, 2018 at 8:52 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Hm, not sure then what would be causing this. It is possible that you're
>> just seeing the best that can be done given the cg conformation. Does it
>> end up minimizing ok?
>>
>> On Wed, Sep 19, 2018 at 2:00 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>> wrote:
>>
>>> Dear Mr Peter,
>>>
>>> I have used text interface to reverse the structure using the value 1
>>> for do_rotations argument. but the structure looks still stretched out.
>>>
>>> Rabeta Yeasmin
>>>
>>>
>>> On Tue, Sep 18, 2018 at 1:36 PM Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>>> wrote:
>>>
>>>> Thanks for your suggestion. I am just reconverting the proteins and
>>>> lipids. I will try the way you suggested soon and let you know what I find.
>>>>
>>>> Rabeta Yeasmin
>>>>
>>>> On Tue, Sep 18, 2018, 12:27 PM Peter Freddolino <petefred_at_umich.edu>
>>>> wrote:
>>>>
>>>>> It looks like the do_rotations argument is set by default in the gui,
>>>>> but just to confirm, could you try doing the reversal via the text
>>>>> interface (see https://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/)
>>>>> for directions). Be sure to specify the value 1 for the do_rotations
>>>>> argument, which should do its best to minimize the perturbations to the
>>>>> reversed structure. Also, are you trying to reverse cg the water and ions?
>>>>> I would not recommend doing so, but rather, reversing the lipid/protein and
>>>>> then re-solvating.
>>>>> Best,
>>>>> Peter
>>>>>
>>>>> On Tue, Sep 18, 2018 at 11:58 AM, Rabeta Yeasmin <
>>>>> rabetayeasmin_at_gmail.com> wrote:
>>>>>
>>>>>> Dear Mr. Peter,
>>>>>>
>>>>>> I have used CG Builder GUI in VMD to reverse the coarse-grained
>>>>>> molecule. That did not ask me to set do_rotations argument. And my system
>>>>>> contains two protein, POPC and POPG lipid, water and ions. I have used the
>>>>>> RBCG model that is provided in VMD 1.9.2 as plugins. I think it is the old
>>>>>> RBCG model from 2007.
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> Rabeta Yeasmin
>>>>>>
>>>>>> On Mon, Sep 17, 2018 at 3:58 PM Peter Freddolino <petefred_at_umich.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> Can you please clarify the precise command that you used to reverse
>>>>>>> coarse grain the molecule? Did you have the do_rotations argument set? What
>>>>>>> does your system contain?
>>>>>>> Also, what CG model are you using? I would hope a recent martini
>>>>>>> version and not the old RBCG model from 2007, unless you're trying to
>>>>>>> precisely reproduce one of those old papers...
>>>>>>> Best,
>>>>>>> Peter
>>>>>>>
>>>>>>> On Mon, Sep 17, 2018 at 12:50 PM, Rabeta Yeasmin <
>>>>>>> rabetayeasmin_at_gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear NAMD users,
>>>>>>>>
>>>>>>>> I have run some coarse-grained simulation of a protein-lipid system
>>>>>>>> in NAMD using residue-based coarse-grained simulation. After running 500ns,
>>>>>>>> I have converted back the last structure of coarse-grained simulation to
>>>>>>>> the all-atom system. But the structure has a lot of stretching. And during
>>>>>>>> the minimization of the converted structure, it showed a lot f warning like-
>>>>>>>> Warning: Tuple 540098 with atoms 20552(159) 20548(159) missing
>>>>>>>> patch 129
>>>>>>>>
>>>>>>>> I have tried another way to overcome this kind of problem. I have
>>>>>>>> minimized the last structure of coarse-grained simulation before
>>>>>>>> converting it to the all-atom system. But that did not work too. Can you
>>>>>>>> please suggest me what can cause this kind of problem?
>>>>>>>> Thanks.
>>>>>>>>
>>>>>>>> Rabeta Yeasmin
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>

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