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
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Received on Wed Jul 11 2012 - 12:00:03 PDT
