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
>>
>> _______________________________________________
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>>
>
>
>
> --
> 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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Received on Wed Jul 11 2012 - 13:00:02 PDT
