Re: [AMBER] problems with "Could not find vdW"

From: Investigador Química <investigacion.faq.gmail.com>
Date: Thu, 9 Oct 2014 10:59:17 -0300

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)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Thu Oct 09 2014 - 07:00:02 PDT
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