From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Jun 27 2013 - 13:18:59 CDT
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 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?
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