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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Wed Sep 19 2018 - 13:00:29 CDT

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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