Re: pKa calculation with thermodynamic integration (TI)

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Tue May 23 2017 - 01:04:17 CDT

Brian,

I already used "set beta" keyword of VMD to assign values for beta. Now I'm
wondering about parameters for dummy atoms. NAMD complains about not
finding vdw parameter for HD atom type, for example. Do I have to manually
assign a value (say 0) for that?

Thanks,
Sadegh

On Wed, May 17, 2017 at 10:54 AM, Radak, Brian K <bradak_at_anl.gov> wrote:

> You can do all of this from inside psfgen now:
>
> patch GLUHD <segid:resid>
> regenerate angles dihedrals
> guesscoord
>
> set atom0List {CG HG1 HG2 CD OE1 HE1 OE2 HE2}
> foreach atom0 $atom0List {
> set atom1 [format "%d1" $atom0] ; # this only works bc of the arbitrary
> naming convention in the patch
> psfset beta $atom0 -1.0
> psfset beta $atom1 1.0
> }
>
> writepsf <psfname>
> writepdb <pdbname> ;# this assigns atom indices to all of the atoms
>
> set ebondsfile [open "foo.extrabonds" "w"]
> foreach atom0 $atom0List {
> set atom1 [format "%d1" $atom0] ;
> set i [expr {segment atomid <segid> <resid> $atom0] - 1}] ;# note the
> index shift
> set j [expr {segment atomid <segid> <resid> $atom1] - 1}]
> puts $ebondsfile [format "bond %d %d %f %f" $i $j 100.0 0.0]
> }
> close $ebondsfile
>
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Hannes Loeffler [Hannes.Loeffler_at_stfc.ac.uk]
> Sent: Wednesday, May 17, 2017 3:37 AM
> To: namd-l_at_ks.uiuc.edu; Sadegh Faramarzi Ganjabad
> Subject: Re: namd-l: pKa calculation with thermodynamic integration (TI)
>
> > Is that what I am supposed to do? if so, how can I tight (for
> > example) CD and CD1 atoms together by a harmonic restraint? at the
> > beginning, there is no distance between them.
>
> You need to mark the outgoing group with -1 in the column that you have
> chosen (alchCol). Look into the extraBonds feature to set additional
> restraints.
>
>
> Cheers,
> Hannes.
>
>

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:18 CST