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

From: Norman Geist (
Date: Fri Sep 21 2018 - 01:08:00 CDT

Are you sure the molecule was whole across PBC bound when you attempted the CG->AA conversion?


Norman Geist


Von: [] Im Auftrag von Peter Freddolino
Gesendet: Donnerstag, 20. September 2018 18:15
An: Rabeta Yeasmin <>
Cc: NAMD list <>
Betreff: Re: namd-l: Bad structure after converting the coarse grained last frame to all-atom


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.




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




On Tue, Sep 18, 2018 at 11:58 AM, Rabeta Yeasmin < <> > 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.




Rabeta Yeasmin


On Mon, Sep 17, 2018 at 3:58 PM Peter Freddolino < <> > 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...



On Mon, Sep 17, 2018 at 12:50 PM, Rabeta Yeasmin < <> > 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?



Rabeta Yeasmin





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