Hi Sandeep,
It is difficult to answer these types of questions. My best guess
is that when you modified the parameter file you introduced an
error. This could happen in a number of ways, each with a different
reported error. Amber was recognizing your files incorrectly and,
which might be a formatting mistake.
If your goal in asking this question is to understand the parameter
files and how leap assigns atom types, charges, et cetera, I suggest
you create from scratch a small parameter set for ethane, and load
only that into leap. Just so you know, this is a difficult task and
will take some time to accomplish.
Best of luck,
Karl
____________________________________
Karl N. Kirschner, Ph.D.
Center for Molecular Design, Co-Director
Department of Chemistry
Hamilton College, Clinton NY 13323
____________________________________
On Mar 8, 2007, at 2:02 AM, Sandeep Kaushik wrote:
> Thanks Karl,
> Getting new files from glycam.ccrc.uga.edu has solved my problem as
> i get TOP and CRD files without any errors now..
> Though, i am still curious for the reason why was i getting those
> FATAL errors ....
> I had just put in the angle and torsional values in the
> glycam04.dat... while the error i got was
> No mass was defined for non-bond atom type: END - ignoring
> i thought removing one "END" from the DAT file would solve the
> problem and it actually did (the error above" Anyway, i tried to
> load the trimannoside using this new modified DAT file , and the
> errors that appeared in LEaP were 'atomtype not found ', as :
> For atom: .R<MAN 949>.A<CM1 1> Could not find type: CG
> This appeared to be unrelated, unless the reason lies in the
> structure of DAT file (line numbers and their content etc.). Please
> tell me the reason....
> Thanks.
>
> On 3/6/07, kkirschn.hamilton.edu <kkirschn.hamilton.edu> wrote: Hi
> Sandeep,
>
> You can find these missing parameters in latest version of the
> Glycam force field, which is downloadable at http://
> glycam.ccrc.uga.edu. You can refer to this force field in you
> leap.in file. For your convenience, I have included the parameters
> below:
>
> CG-OH-HO 55.00 109.50 Methanol
>
> OH-CG-OS-CG 1 0.55 300.0 -1. Copy of
> OS-CG-OS-CG (not derived)
> 1 0.60 0.0
> -2.
> 1 0.20 60.0 3.
>
> Glycam was originally created to simulate sugars terminated with a
> methoxy group or be attached to a protein at the C1 position, instead
> of a hydroxyl group.
>
> As for the issues arising from the use of Insight II, I am not sure
> as to what is going on. Mixing programs can lead you into a whole
> nest of troubles due to changes in atom type and residue names. If
> you redo your initial methodology, sticking only with AMBER and using
> the new force field, you should be fine. Look around the glycam
> website, because there are a lot of tools that one can use when
> performing MD simulations involving carbohydrates.
>
> The manuscript describing the Glycam force field is currently being
> peer reviewed. Please keep an eye out for its publication.
>
> Cheers,
> Karl
>
> ____________________________________
> Karl N. Kirschner, Ph.D.
> Center for Molecular Design, Co-Director
> Department of Chemistry
> Hamilton College, Clinton NY 13323
> ____________________________________
>
> On Mar 6, 2007, at 7:44 AM, Sandeep Kaushik wrote:
>
> > Hi,
> > I am using AMBER9 on an HP machine and want to include a
> > trimannoside in my MD simulation. So i have created an OFF file of
> > it as MAN.lib where i have specified the atom types and charges
> > according to glycam04 force field. However in the absence of an
> > angle <<O5-C1-O1>> (as none of the units of Glycam04 has it)
> > and hence the dihedral angle <<O5-C1-O1-H1>> i get the error
> > message upon saving the top and crd files as follows....
> > ...................
> > .....................
> > Checking Unit.
> > ERROR: The unperturbed charge of the unit: -47.160000 is not
> integral.
> > WARNING: The unperturbed charge of the unit: -47.160000 is not zero.
> > ERROR: The perturbed charge: -47.160000 is not integral.
> > WARNING: The perturbed charge: -47.160000 is not zero.
> > -- ignoring the errors and warnings.
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Could not find angle parameter: OH - CG - OS
> > Building proper torsion parameters.
> > ** No torsion terms for CG-OS-CG-OH
> > Building improper torsion parameters.
> > total 2880 improper torsions applied
> > Building H-Bond parameters.
> > Parameter file was not saved.
> >
> > So I inorder to be able to modify the glycam04.dat file i copied it
> > to a new directory along with the glycam04.in and determined the
> > Angle and Dihedral values using INSIGHT II. (& K theta, n, V, and
> > Phi0 values were randomly picked from glycam04.dat file just to
> > check whether it works or not?). THen i modified glycam04.dat and
> > tired to load the molecule again, only to get
> > another error message as follows..
> >
> > GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
> > No mass was defined for non-bond atom type: END - ignoring
> > Loading Prep file: ./glycam04.in
> >
> > I could remove this message (in bold face) by deleting the one out
> > of two repeating words "END" in the glycam.dat file but i guess
> > that it is not correct to do so as the original glycam04.dat file
> > has both words. And upon saving the parmtop and crd files i get the
> > error message...
> >
> > Checking Unit.
> > ERROR: The unperturbed charge of the unit: -47.160000 is not
> integral.
> > WARNING: The unperturbed charge of the unit: -47.160000 is not zero.
> > ERROR: The perturbed charge: -47.160000 is not integral.
> > WARNING: The perturbed charge: -47.160000 is not zero.
> >
> > -- ignoring the errors and warnings.
> >
> > Building topology.
> > Building atom parameters.
> > For atom: .R<MAN 949>.A<CM1 1> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM2 2> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM3 3> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM4 4> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM5 5> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM6 6> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM7 12> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM8 13> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM9 14> Could not find type: CG
> > For atom: .R<MAN 949>.A<CM0 15> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMA 16> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMB 17> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMC 24> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMD 25> Could not find type: CG
> > For atom: .R<MAN 949>.A<CME 26> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMF 27> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMG 28> Could not find type: CG
> > For atom: .R<MAN 949>.A<CMH 29> Could not find type: CG
> > Parameter file was not saved.
> >
> > Plz tell me how to make LEaP recognize this trimannoside without
> > giving errors while saving the parmtop and crd files for my MD
> > simulation...
> ----------------------------------------------------------------------
> -
>
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Received on Sun Mar 11 2007 - 06:07:16 PDT
