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 Wed Mar 07 2007 - 06:07:44 PST
