From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Jun 27 2013 - 23:35:21 CDT
I still be thankful to everyone who can provide me with the NAMD tutorial
for the protein-ligand simulation and subsequent analysis ( In particular
I'm interesting in the dynamics of the Hbonds between protein and ligand
during simulation RUN).
2013/6/28 JC Gumbart <gumbart_at_ks.uiuc.edu>
> 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:
> 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,
> 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
>>> in the topology new bond between O3 and P looks strange :)
>> Can you be a bit more specific? What looks strange about this bond?
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