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

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Tue Sep 18 2018 - 13:36:40 CDT

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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