Can you send me your topology file? It's possible there is another issue
that I didn't catch.
(If you also send a parmed script along with what you expected to happen,
that would be great).
Thanks!
Jason
On Wed, Jul 11, 2012 at 3:44 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> I've recompiled already. Just to make sure, I've erased amber12
> directory, re-extracted, applied patches and then recompiled. Still
> didn't change the prmtop hydroxyl parameters. The strange thing is
> that it changes the parameters for other atoms. I've tried on the zinc
> atom and it worked fine.
> Maybe it has something to do with the name, or something like this.
> Fabrício Bracht
>
> 2012/7/11 Jason Swails <jason.swails.gmail.com>:
> > You need to recompile after you apply bugfix.14.
> >
> > You can do this for parmed alone by doing:
> >
> > cd $AMBERHOME/AmberTools/src/parmed && make
> >
> > Then try again...
> >
> > Also, you can specify atom types via .% (instead of just . for atom
> names).
> > So your parmed command would be:
> >
> > changeLJSingleType :340.%Ho 0.2 0.03
> >
> > HTH,
> > Jason
> >
> > On Wed, Jul 11, 2012 at 2:28 PM, Fabrício Bracht <bracht.iq.ufrj.br>
> wrote:
> >
> >> Applied patch 14 and it did not work out. Am I doing something wrong.
> >> I opened the prmtop file with parmed.py
> >> Then I tried
> >> > changeLJSingleType :340.Ho 0.2 0.03
> >> It didn't work. But that was my fault, as I later discovered that Ho
> >> is the type and H1 is the name, so I tried again:
> >> > changeLJsingletype :340.H1 0.2 0.03
> >> Then, the usual phrase saying that the radius and the well depth had
> >> been change.
> >> After that I applied to the other active site hydroxyl hydrogen
> >> > changeLJsingleType :342.H1 0.2 0.03
> >> All working out until now.
> >> > outparm changedtop.prmtop
> >> No errors until now. So, I decided to check on my newly created
> >> changedtop.prmtop.
> >> $ parmed.xy changedtop.prmtop
> >> > printdetails :340
> >> It prints out the residue details and, for my surprise, the parameters
> >> 0.000 and 0.000 for radius and well depth are still there.
> >> It happens the same when I ask it to write a new frcmod file.
> >> Thank you
> >> Fabrício Bracht
> >>
> >> 2012/7/8 Jason Swails <jason.swails.gmail.com>:
> >> > On Sun, Jul 8, 2012 at 2:41 AM, Fabrício Bracht <bracht.iq.ufrj.br>
> >> wrote:
> >> >
> >> >> SG ( SH) 5311 ZN ( ZN) 2.3440 73.7200
> >> >> ZN ( ZN) 5312 O ( OH) 1.9240 140.4500
> >> >> Strangely though, the md methot frcmod file didn't have any bond
> >> >> parameters for the O - Ho bond. Do you think it is safe to use the
> 553
> >> >> from the other method?
> >> >>
> >> >> The thing with the lennard-jones parameters is this. I had written at
> >> >> the end of the frcmod file lines containing ljparam for Ho (MCPB had
> >> >> already written parameters for sulfur, so, I'm not counting that
> one).
> >> >> When I do the whole leap routine, (loadamberparams myparam.frcmod and
> >> >> loadamberprep myprep.prep, etc etc) everything works fine. I set up
> >> >> the bonds with the bond command, and finally get my prmtop and inpcrd
> >> >> files.
> >> >> Once I use xparmed.py to check the prmtop file, I get the info that
> my
> >> >> Ho atom does not have the parameters I have specified for it. It
> still
> >> >> shows up as having 0.000 and 0.000 for well depth and radius. Leap
> >> >> does not exit with an error message, and to make sure, I have done
> the
> >> >> whole thing again and got the same thing. I tried also to rename the
> >> >> Ho atom (hoping that leap was misunderstanding my Ho for HO, which
> has
> >> >> 0.000 for params), and that didn't work out as well. When I try to
> >> >> change the values using "changeLJsingetype" command from parmed.xy, I
> >> >> get :
> >> >>
> >> >> Changing :342.Ho Lennard-Jones well depth from 0.0000 to 0.0300
> >> >> (kal/mol) and radius from 0.0000 to 0.2000
> >> >>
> >> >
> >> > I can verify that this does not work as expected. (A problem being
> that
> >> > None and 0 both evaluate to logical False in Python, so this is a
> special
> >> > case). I will release a patch for this shortly.
> >> >
> >> > Thanks!
> >> > Jason
> >> >
> >> > --
> >> > Jason M. Swails
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Candidate
> >> > 352-392-4032
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 11 2012 - 13:00:03 PDT
