Hi Jason. I've sent the email with my topology file. Did you receive?
Thanks
Fabrício Bracht
2012/7/11 Jason Swails <jason.swails.gmail.com>:
> 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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>>
>
>
>
> --
> 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 - 17:30:03 PDT
