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 - 06:07:38 PST
