Re: Strange Bond Behavior Question

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Sat Jun 23 2018 - 04:54:04 CDT

It probably means that VMD is guessing the bonds based on distances.
You should always load a proper topology (psf file) first.
Best,
Ajasja

On Fri, 22 Jun 2018 at 23:57, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> One more thing I should mention. I loaded the DCD onto the PDB file and
> that's when I see the odd effects. However, if I load the PSF and load the
> DCD onto that, I don't see those strange bond effects. What does that mean?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* João Ribeiro <jribeiro_at_ks.uiuc.edu>
> *Sent:* Friday, June 22, 2018 3:08:07 PM
> *To:* namd-l_at_ks.uiuc.edu; McGuire, Kelly
> *Cc:* Vmd l
> *Subject:* Re: namd-l: Strange Bond Behavior Question
>
> Hi Kelly,
>
> that really sounds strange, especially because "They seem to be stretching
> and bonding to other lipid atoms"
> is
> vague and creation of bonds is impossible.
> ​ ​
> Now, if you generated the bilayer in CHARMM-GUI, I am pretty sure that the
> boundary conditions will be wrong. QwikMD doesn't have a way to detect the
> axis of membranes generated by other programs, so I will assume that you
> have water surrounding your system, even the hydrophobic region of the
> membrane.
>
> What happens if you run the simulation with the psf and pdb files
> generated by CHARMM-GUI? Do you observe the same? If you don't, I would
> suggest for you to use those psf and pdb files with the configuration files
> originated by CHARMM-GUI, or use QwikMD configuration files as templates,
> changing the necessary information about your system.
>
> Best
>
> Joao
>
>
> On Fri, Jun 22, 2018 at 3:46 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
> This is a question for both VMD and NAMD support, so I am sending it to
> both. I used QwikMD to set up a simulation, and
>
> something I have never seen before has occurred. I placed a membrane
> protein in a 100x100 DMPC bilayer using
>
> CHARMM-GUI, and then I used that PDB to set up a simulation in QwikMD.
> Upon observation of the minimization, annealing, and
>
> equilibration DCD files, I noticed the lipid bonds doing something very
> odd. They seem to be stretching and bonding to other
>
> lipid atoms. I tried attaching pictures, but I don't see it posted to the
> mailing list. I didn't change anything in the minimize, anneal,
>
> and equilibrate scripts that QwikMD produces, and I've never seen this
> before with those simulations with these generated scripts...
>
>
>
>
>
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>

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