Just checked it, it works now.
Thanks!
Jason
(I'll also check in a new frcmod.constph without the blank line)
On Sun, Feb 28, 2010 at 3:49 PM, Wei Zhang <zgjzweig.gmail.com> wrote:
> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>
>>
>>
>> --
>> ---------------------------------------
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
---------------------------------------
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 - 13:30:02 PST
