[gmx-users] oligosaccharide oplsaa .itp

[Mark Abraham]

On 12/25/2011 7:56 PM, Ashalatha Sreshty wrote:
> Dear All,
>
> I have a problem running gromacs for a oligosaccharide. it has 14
> units sugars containing glucose, mannose and N-acetyl glucosamine
> units. I want to do MD simulations for this with opls aa force field.
> For this I have generated the .itp files using topolgen (edited the
> atoms according to the opls atoms types) but when I am executing
> grompp command the following error comes up:
>
> ERROR 226 [file 901opls.itp, line 2897]:
>  No default Ryckaert-Bell. types

The R-B dihedral defined on line 2897 does not have parameters 
associated with it on that line, and grompp could find none for the atom 
types involved back in the [dihedraltypes] section of the force field. 
You'll have to do some detective work to find out why.

> ERROR 227 [file 901opls.itp, line 2902]:
>  No default Ryckaert-Bell. types
> ERROR 228 [file 901opls.itp, line 2903]:
>  No default Ryckaert-Bell. types
> ERROR 229 [file 901opls.itp, line 2904]:
>  No default Ryckaert-Bell. types
>
> Excluding 3 bonded neighbours molecule type 'DRG'
>
> NOTE 1 [file 901opls.top, line 19]:
>  System has non-zero total charge: -2.177100e+01

You have a net charge of -21.771, so your topologies are mangled somehow.

Mark

>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> There was 1 note
>
> ------------------------------
> -------------------------
> Program grompp_d, VERSION 4.0.5
> Source code file: grompp.c, line: 986
>
> Fatal error:
> There were 229 errors in input file(s)
>
> These are the lines of the dihedrals in .itp file
>
> I do not understand what to do next. Please help me resolve this problem
> and also educate me how to assign opls forcefield to carbohydrates for
> MD simulations. Thank you in advance.
>
> AshaLatha Sreshty
> Molecular Sciences Laboratory
> National Institute of Immunology
> New Delhi, India
>
>
>
>
>


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