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
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Received on Wed Jul 11 2012 - 12:30:04 PDT
