Re: Protein-ligand simulation

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jun 27 2013 - 18:40:15 CDT

You're asking many questions that may be best answered by reading through the various tutorials, user guides, previous posts on the mailing lists, and literature as well as some trial and error. Then if something still is unclear, you should come back here and ask, explaining what you tried and what didn't work. I don't mean to discourage you by any means, but rather ENCOURAGE you to avail yourself of the numerous resources into which a great deal of time was already devoted. Personally, I feel like this will be more useful in the long run.

I sincerely hope I don't send you running back to gromacs! I understand a new program can be daunting (ever try to run charmm for the first time? ;) But the tutorials are immensely helpful, I assure you.

On Jun 27, 2013, at 2:18 PM, James Starlight wrote:

> Kenno,
>
> thanks again for suggestion.
>
> By the way could someone tell me how ligand topology (psf file) should be included in the namd's conf file ? For example I have system consited of solvated protein with ions (for that system I have psf file).
> Than I've done parametrization for my ligand (obtaining pdb as well as psf files ). Assuming that my ligand is in the correct pose regarding protein I can merge both pdb files. But how I should merge both psf files ( or should I include both of them in the conf file separately ? )
>
> Thanks for help,
>
> James
>
> 2013/6/27 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
> On 06/27/2013 01:16 AM, James Starlight wrote:
> psfgen) total of 34 atoms
> psfgen) total of 37 bonds
> psfgen) total of 66 angles
> psfgen) total of 99 dihedrals
> psfgen) total of 3 impropers
> psfgen) total of 0 cross-terms
>
> Those are the correct sums as also seen in CHARMM.
>
>
> Here you can see that dihedrals and angles for new bond were also included
> in the topology new bond between O3 and P looks strange :)
>
> Can you be a bit more specific? What looks strange about this bond?
>
> Cheers,
>
> Kenno.
>
>

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