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 Sun Jul 08 2012 - 11:00:02 PDT
