AMBER Archive (2005)

Subject: Re: AMBER: Atom type problem

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 11 2005 - 11:40:12 CDT

Hi Nagara,

I have tried to create the .prmtop and .inpcrd files. I created the .prepi
file from the data u send in your prev email. There were some unknown atom
types (C2, C3, and CH). I checked out the parm99.dat, and yes, they are
not defined in this force field. I checked out the ff03 force field, and
they arent defined in that force field, either.

You have to create the missing parameters in an .frcmod file, if you want
those atoms to have a different atom type. Where did you get this .prepi
file? U might find the modified .frcmod file in the place where u got this
.prepi file. Otherwise, it is really hard to define the missing parameters
for a new atom type. Good luck.

Best,

PS: On second thought, I checked out the paper u provided. And yes, they
have the missing parameters in that paper. U have to create an .frcmod
file, which will include all those missing parameters. There might be
already an .frcmod file for this particular structure in internet. If not,
you can create it by yourself. In order to that, read the "Force field
parameter modification file specification" part of
        http://amber.scripps.edu/formats.html

As for an example, check out the following files:

        $AMBERHOME/dat/leap/parm/frcmod.*

Hope this helps. Best...

On Thu, 11 Aug 2005, nag raj wrote:

> Dear Yildirim,
> Thank you for your reply. I am using
> leaprc.ff99 force field and I took parameters like
> bond length, bond angle and dihegral angle parameters
> from reference "journal of computational chemistry,
> vol 20, 531-545, 1999".
> Thank you
> bye
> nagaraju
>
> --- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
>
> > Dear Nagara,
> >
> > Which force field are you using?
> >
> > On Thu, 11 Aug 2005, nag raj wrote:
> >
> > > Dear amber users,
> > > I am trying to assign parameters
> > for
> > > DPPC molecule. While saving, i am getting the
> > > following error.
> > >
> > > For atom: .R<DPP 1>.A<N2 1> Could not find type:
> > N3
> > > For atom: .R<DPP 1>.A<C4 2> Could not find type:
> > C3
> > > For atom: .R<DPP 1>.A<C3 3> Could not find type:
> > C3
> > > For atom: .R<DPP 1>.A<C1 4> Could not find type:
> > C3
> > > For atom: .R<DPP 1>.A<C5 5> Could not find type:
> > C2
> > > For atom: .R<DPP 1>.A<C6 6> Could not find type:
> > C2
> > > For atom: .R<DPP 1>.A<O7 7> Could not find type:
> > OS
> > > ..... ........ .........
> > > ....... ....... ..........
> > > Before loading prep and frcmod files i used the
> > > addatom type command.
> > >
> > > addAtomTypes {
> > > { "C3" "C" "sp3" }
> > > { "C2" "C" "sp3" }
> > > { "CH" "C" "sp3" }
> > > { "C" "C" "sp2" }
> > > { "OS" "O" "sp3" }
> > > { "O" "O" "sp2" }
> > > { "O2" "O" "sp2" }
> > > { "P" "P" "sp3" }
> > > { "N3" "N" "sp3" }
> > >
> > > In this case also i am getting same problem.
> > > Would you tell me how to solve this pboblem.
> > >
> > > Here is pdb, prep files.
> > >
> > > PREP-FILE:
> > >
> > > 0 0 2
> > >
> > > This is a remark line
> > > molecule.res
> > > DPP XYZ 0
> > > CHANGE OMIT DU BEG
> > > 0.0000
> > > 1 DUMM DU M 999.000 999.0
> > > -999.0 .00000
> > > 2 DUMM DU M 999.000 -999.0
> > > 999.0 .00000
> > > 3 DUMM DU M -999.000 999.0
> > > 999.0 .00000
> > > 4 N2 N3 M -11.075000 8.458000
> > > 1.343000 -0.50000
> > > 5 C4 C3 E -10.735000 8.819000
> > > -0.107000 0.40000
> > > 6 C3 C3 E -10.402000 9.434000
> > > 2.275000 0.40000
> > > 7 C1 C3 E -12.585000 8.550000
> > > 1.495000 0.40000
> > > 8 C5 C2 M -10.668000 6.978000
> > > 1.637000 0.30000
> > > 9 C6 C2 M -9.154000 6.725000
> > > 1.768000 0.40000
> > > 10 O7 OS M -8.451000 6.756000
> > > 0.539000 -0.80000
> > > 11 P8 P M -8.982000 5.710000
> > > -0.594000 1.70000
> > > 12 O10 O2 E -9.532000 4.516000
> > > 0.138000 -0.80000
> > > 13 O9 O2 E -9.858000 6.519000
> > > -1.512000 -0.80000
> > > 14 O11 OS M -7.581000 5.376000
> > > -1.319000 -0.70000
> > > 15 C12 C2 M -6.621000 4.616000
> > > -0.600000 0.40000
> > > 16 C13 CH M -6.003000 3.575000
> > > -1.538000 0.30000
> > > 17 O14 OS S -7.041000 2.613000
> > > -1.837000 -0.70000
> > > 18 C15 C B -6.811000 1.722000
> > > -2.828000 0.70000
> > > 19 C17 C2 S -7.957000 0.745000
> > > -2.965000 0.00000
> > > 20 C18 C2 S -8.593000 0.386000
> > > -1.621000 0.00000
> > > 21 C19 C2 S -9.611000 -0.749000
> > > -1.750000 0.00000
> > > 22 C20 C2 S -10.300000 -1.009000
> > > -0.408000 0.00000
> > > 23 C21 C2 S -11.390000 -2.080000
> > > -0.483000 0.00000
> > > 24 C22 C2 S -10.835000 -3.496000
> > > -0.645000 0.00000
> > > 25 C23 C2 S -11.963000 -4.532000
> > > -0.611000 0.00000
> > > 26 C24 C2 S -11.414000 -5.957000
> > > -0.661000 0.00000
> > > 27 C25 C2 S -12.541000 -6.991000
> > > -0.606000 0.00000
> > > 28 C26 C2 S -11.983000 -8.413000
> > > -0.557000 0.00000
> > > 29 C27 C2 S -13.100000 -9.456000
> > > -0.487000 0.00000
> > > 30 C28 C2 S -12.525000 -10.869000
> > > -0.373000 0.00000
> > > 31 C29 C2 S -13.627000 -11.925000
> > > -0.302000 0.00000
> > > 32 C30 C2 S -13.035000 -13.329000
> > > -0.163000 0.00000
> > > 33 C31 C3 E -14.123000 -14.388000
> > > -0.096000 0.00000
> > > 34 O16 O E -5.818000 1.710000
> > > -3.546000 -0.70000
> > > 35 C32 C2 M -4.811000 2.884000
> > > -0.861000 0.50000
> > > 36 O33 OS M -5.292000 2.056000
> > > 0.212000 -0.70000
> > > 37 C34 C M -4.337000 1.340000
> > > 0.859000 0.80000
> > > 38 O36 O E -3.131000 1.479000
> > > 0.722000 -0.60000
> > > 39 C35 C2 M -4.983000 0.281000
> > > 1.716000 0.00000
> > > 40 C37 C2 M -5.104000 -1.009000
> > > 0.913000 0.00000
> > > 41 C38 C2 M -5.902000 -2.079000
> > > 1.658000 0.00000
> > > 42 C39 C2 M -5.953000 -3.376000
> > > 0.848000 0.00000
> > > 43 C40 C2 M -6.775000 -4.457000
> > > 1.552000 0.00000
> > > 44 C41 C2 M -6.739000 -5.768000
> > > 0.761000 0.00000
> > > 45 C42 C2 M -7.595000 -6.849000
> > > 1.422000 0.00000
> > > 46 C43 C2 M -7.440000 -8.235000
> > > 0.784000 0.00000
> > > 47 C44 C2 M -7.825000 -8.278000
> > > -0.695000 0.00000
> > > 48 C45 C2 M -7.692000 -9.666000
> > > -1.333000 0.00000
> > > 49 C46 C2 M -8.674000 -10.706000
> > > -0.785000 0.00000
> > > 50 C47 C2 M -8.019000 -11.700000
> > > 0.177000 0.00000
> > > 51 C48 C2 M -9.047000 -12.697000
> > > 0.717000 0.00000
> > > 52 C49 C2 M -8.402000 -13.719000
> > > 1.651000 0.00000
> > > 53 C50 C3 M -9.428000 -14.708000
> > > 2.183000 0.00000
> > >
> > >
> > > LOOP
> > >
> > > IMPROPER
> > > C17 O16 C15 O14
> > > C35 O36 C34 O33
> > >
> > > DONE
> > > STOP
> > >
> > >
> > > Here is the Pdb file:
> > >
> > >
> > > ATOM 1 N2 DPP 1 -11.075 8.458
> > 1.343
> > > 1.00 -1.01
> > > ATOM 2 C5 DPP 1 -10.668 6.978
> > 1.637
> > > 1.00 0.50
> > > ATOM 3 C6 DPP 1 -9.154 6.725
> > 1.768
> > > 1.00 0.28
> > > ATOM 4 O7 DPP 1 -8.451 6.756
> > 0.539
> > > 1.00 -0.55
> > > ATOM 5 P8 DPP 1 -8.982 5.710
> > -0.594
> > > 1.00 1.44
> > > ATOM 6 O11 DPP 1 -7.581 5.376
> > -1.319
> > > 1.00 -0.55
> > > ATOM 7 C12 DPP 1 -6.621 4.616
> > -0.600
> > > 1.00 0.28
> > > ATOM 8 C13 DPP 1 -6.003 3.575
> > -1.538
> > > 1.00 0.28
> >
> === message truncated ===
>
>
>
>
> ____________________________________________________
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>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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