Hi,
Seems like the formatting in your frcmod file is not correct. Did you
forget to give it a title? Refer to here for some more info:
http://ambermd.org/formats.html#parm.dat
particularly the 'Force field parameter modification file
specification' section. You can also look at some examples of working
frcmod files in $AMBERHOME/dat/leap/parm.
Hope this helps,
-Dan
On Wed, Oct 8, 2014 at 9:07 AM, Investigador Química
<investigacion.faq.gmail.com> wrote:
> I'm sorry, I was wrong. The error is like in the photograph that I attached.
>
>
> 2014-10-08 11:51 GMT-03:00 Jason Swails <jason.swails.gmail.com>:
>
>> On Wed, 2014-10-08 at 11:40 -0300, Investigador Química wrote:
>> > Hi amber users.
>> >
>> > I have a problem when I trying to define an atom type in the parm99.dat
>> > and leaprc.ff99SB.
>> >
>> > Amber not read the atom type that I defined, so I have problems like this
>> > (for example):
>> >
>> >
>> > Building topology.
>> > Building atom parameters.
>> > Building bond parameters.
>> > Could not find bond parameter for: SH - SH
>> > Could not find bond parameter for: SH - SH
>> > Building angle parameters.
>> > Could not find angle parameter: HS - SH - SH
>> > Could not find angle parameter: HS - SH - SH
>> > Could not find angle parameter: SH - SH - 2C
>> > Could not find angle parameter: SH - SH - HS
>> > Could not find angle parameter: SH - SH - 2C
>> > Could not find angle parameter: SH - SH - HS
>> > Could not find angle parameter: 2C - SH - SH
>> > Could not find angle parameter: 2C - SH - SH
>>
>> You get these errors as a result of not preparing your PDB files that
>> contain disulfide bonds correctly for tleap.
>>
>> As you can see, there are no errors about the CH and OH atom types.
>> Paying close attention to the error messages can help prevent you from
>> chasing down problems that don't exist.
>>
>> Also, if you pop one of those error messages into Google, you should be
>> pointed to the appropriate solution. That's always a good thing to try
>> first:
>>
>> Could not find bond parameter for: SH - SH
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> 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
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 08 2014 - 08:30:04 PDT
