Hi All,
Just fixed the bug of reading frcmod.constph and checked in.
Sorry it took so long.
Just in case you are interested: the bug rises because there is
an extra empty line between title and the angle section. i.e:
Force field modifcations for titrations
ANGLE
Of all the frcmod files under amber11/dat/leap/parm, frcmod.constph
is the only one in this format. (In all other frcmod files, the first section
is immediately following the title, thus we might consider change frcmod.constph
too)
Sincerely,
Wei
On Feb 23, 2010, at 9:40 AM, Jason Swails wrote:
> This is not solving the problem...
>
> [gtkleap]$ loadamberparams frcmod.constph
> [gtkleap]$ loadoff constph.lib
> [gtkleap]$ [gtkleap]$ l = sequence {ACE AS4 NME}
> Sequence: ACE
> Sequence: AS4
> tail: 5 C
> head: 7 N
> Sequence: NME
> tail: 18 C
> head: 23 N
> [gtkleap]$ [gtkleap]$ saveamberparm l prm crd
> angl parm not found for AS4:OD1-AS4:CG-AS4:OD2
> Error: can't find parameter for angl OH-C-OH
>
>
> I copied your version of frcmod.constph into both
> $AMBERHOME/dat/leap/parm and into my local directory, as well as
> running the commands interactively.
>
> On Tue, Feb 23, 2010 at 10:20 AM, case <case.biomaps.rutgers.edu> wrote:
>> On Tue, Feb 23, 2010, Jason Swails wrote:
>>>
>>> I'm having some difficulties setting up constant pH-ready prmtops in
>>> sleap (whereas I have no problems in tleap). The simple script below
>>> works with tleap, but with sleap complains about not finding
>>> parameters for OH-C-OH. This parameter is defined in frcmod.constph
>>> located in $AMBERHOME/dat/leap/parm . I tried moving the frcmod to
>>> the current working directory and re-running the script, but it still
>>> doesn't work. Any ideas?
>>
>> There is several typos in the frcmod.constph file; try the following in
>> its place:
>>
>> Force field modifcations for titrations
>>
>> ANGLE
>> HO-OH-HO 60.000 134.000
>> OH-C -OH 80.0 120.0
>>
>> IMPROPER
>> X -X -OH-HO 0 1.000 180.000 2.000
>> CT-OH-C -OH 0 10.5 180. 2.
>>
>>
>> Basically, single letter atom types are supposed to be left-justified; see
>> the parm99.dat file, for example.
>>
>> If that solves the problem, can you check in the updated frcmod file?
>>
>> ...thanks..dave
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Sun Feb 28 2010 - 13:00:03 PST
