Hi,
You really need to make sure you're following the format exactly. One
major problem is that your section titles are all followed by blank
lines, which indicates the end of a section. So this:
MASS
C 12.01 0.616
should be:
MASS
C 12.01 0.616
I strongly suggest looking at a few of the many frcmod files in
$AMBERHOME/dat/leap/parm so you can be sure you are correctly
following the format.
Hope this helps,
-Dan
On Thu, Oct 9, 2014 at 7:59 AM, Investigador Química
<investigacion.faq.gmail.com> wrote:
> Here is the force files defined for me. This is attached.
> First I run the xleap
> then I load the pdb file with: ntdox = loadpdb ntdox.pdb
> then I load the atom charge file and atom type file with:
>
> source setypentdox.dat
> source setchargentdox.dat
>
> To this step all is ok.
> Then I load the frcmod file with:
>
> frc = loadamberparams frcntdox.frcmod (this file is attached)
>
> and the system says:
>
> frc=loadamberparams frcntd.frcmod
> Loading parameters: ./frcntd.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> MASS
> Unknown keyword: C 12.01 in parameter file. Perhaps a format error?
> Unknown keyword: CA 12.01 in parameter file. Perhaps a format error?
> Unknown keyword: CT 12.01 in parameter file. Perhaps a format error?
> Unknown keyword: HA 1.008 in parameter file. Perhaps a format error?
> Unknown keyword: HC 1.008 in parameter file. Perhaps a format error?
> Unknown keyword: HO 1.008 in parameter file. Perhaps a format error?
> Unknown keyword: NT 14.006 in parameter file. Perhaps a format error?
> Unknown keyword: O 15.999 in parameter file. Perhaps a format error?
> Unknown keyword: OH 15.999 in parameter file. Perhaps a format error?
> Unknown keyword: OS 15.999 in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA 3 in parameter file. Perhaps a format error?
> Unknown keyword: CA-HA 3 in parameter file. Perhaps a format error?
> Unknown keyword: CA-CT 3 in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT 3 in parameter file. Perhaps a format error?
> Unknown keyword: CT-OS 3 in parameter file. Perhaps a format error?
> Unknown keyword: CT-HC 3 in parameter file. Perhaps a format error?
> Unknown keyword: CT-OH 3 in parameter file. Perhaps a format error?
> Unknown keyword: CT-NT 3 in parameter file. Perhaps a format error?
> Unknown keyword: CT-C 3 in parameter file. Perhaps a format error?
> Unknown keyword: O -HO 3 in parameter file. Perhaps a format error?
> Unknown keyword: OH-HO 3 in parameter file. Perhaps a format error?
> Unknown keyword: C -O 3 in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-OH in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-HC in parameter file. Perhaps a format error?
> Unknown keyword: CT-C -CT in parameter file. Perhaps a format error?
> Unknown keyword: CT-C -O in parameter file. Perhaps a format error?
> Unknown keyword: CT-OH-HO in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CA in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CT in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-HA in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-OH in parameter file. Perhaps a format error?
> Unknown keyword: CA-CT-CT in parameter file. Perhaps a format error?
> Unknown keyword: CA-CT-HC in parameter file. Perhaps a format error?
> Unknown keyword: CA-HA-CA in parameter file. Perhaps a format error?
> Unknown keyword: CA-OH-HO in parameter file. Perhaps a format error?
> Unknown keyword: CA-OH-OH in parameter file. Perhaps a format error?
> Unknown keyword: CT-C -O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-HC in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-NT in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-OH in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-OS in parameter file. Perhaps a format error?
> Unknown keyword: CT-OH-HO in parameter file. Perhaps a format error?
> Unknown keyword: CT-OS-CT in parameter file. Perhaps a format error?
> Unknown keyword: OS-CT-OS in parameter file. Perhaps a format error?
> Unknown keyword: CA-HA-CA-H in parameter file. Perhaps a format error?
> Unknown keyword: CA-HA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-HA-C in parameter file. Perhaps a format error?
> Unknown keyword: HA-CA-CA-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-C -CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-C -CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-C -CT-O in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-OH-H in parameter file. Perhaps a format error?
> Unknown keyword: C -CT-OH-H in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CA-H in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CA-O in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CA-O in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-OH-H in parameter file. Perhaps a format error?
> Unknown keyword: CA-CA-OS-C in parameter file. Perhaps a format error?
> Unknown keyword: CA-CT-OS-C in parameter file. Perhaps a format error?
> Unknown keyword: CA-OS-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-C -C in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-C -O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-OH-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-CA-CA-O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-OS-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-OS-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-OS-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-OS-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-NT-H in parameter file. Perhaps a format error?
> Unknown keyword: CT-CT-OS-C in parameter file. Perhaps a format error?
> Unknown keyword: CT-OS-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: HA-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: HA-CA-CA-H in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-OH-H in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-OS-C in parameter file. Perhaps a format error?
> Unknown keyword: HC-CT-NT-H in parameter file. Perhaps a format error?
> Unknown keyword: NT-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: NT-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: NT-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: NT-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: O -C -CT-O in parameter file. Perhaps a format error?
> Unknown keyword: O -C -CT-H in parameter file. Perhaps a format error?
> Unknown keyword: O -CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: OH-CT-C -C in parameter file. Perhaps a format error?
> Unknown keyword: OH-CT-C -O in parameter file. Perhaps a format error?
> Unknown keyword: OH-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: OH-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: OH-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: OH-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: OS-CA-CA-C in parameter file. Perhaps a format error?
> Unknown keyword: OS-CA-CA-H in parameter file. Perhaps a format error?
> Unknown keyword: OS-CT-CT-C in parameter file. Perhaps a format error?
> Unknown keyword: OS-CT-CT-H in parameter file. Perhaps a format error?
> Unknown keyword: OS-CT-CT-O in parameter file. Perhaps a format error?
> Unknown keyword: OS-CT-OS-C in parameter file. Perhaps a format error?
>> check ntdox
> Checking 'ntdox'....
> Checking parameters for unit 'ntdox'.
> Checking for bond parameters.
> Could not find bond parameter for: CA - OS
> Could not find bond parameter for: CA - O
> Could not find bond parameter for: CA - O
> Could not find bond parameter for: NT - HO
> Could not find bond parameter for: NT - HO
> Checking for angle parameters.
> Could not find angle parameter: CA - OS - CT
> Could not find angle parameter: CA - CA - OS
> Could not find angle parameter: CA - CA - O
> Could not find angle parameter: CA - CA - O
> Could not find angle parameter: CA - CA - OS
> Could not find angle parameter: CA - CA - O
> Could not find angle parameter: CA - CA - O
> Could not find angle parameter: CA - CT - OS
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: OH - CT - C
> Could not find angle parameter: C - CT - OH
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: OH - CT - HC
> Could not find angle parameter: OH - CT - HC
> Could not find angle parameter: CT - NT - HO
> Could not find angle parameter: CT - NT - HO
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: OS - CT - HC
> Could not find angle parameter: HC - CT - NT
> Could not find angle parameter: OH - CT - HC
> Could not find angle parameter: HO - NT - HO
> There are missing parameters.
>
>
>
> So i don't to do.
>
>
>
> 2014-10-08 12:15 GMT-03:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> 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
>>
>
> _______________________________________________
> 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)
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Received on Thu Oct 09 2014 - 07:30:02 PDT
