Re: [gmx-users] MD simulation of Glycoproteion

[Mark Abraham]

On 15/12/2011 1:05 PM, ??? wrote:

Dear gromacs users
 I used Gromacs in order to get a MD simulation of 
Glycoproteion.now I have got the Glycoproteion's PDB file,When I want 
to MD by GMX,it gave a Warnning:Fatal error: Residue ""not found 
in residue topology database.


So check out 
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database 
like it probably suggested.


And I know it was because of the force field,I want to know which 
force field should be choose in GMX,And where I can get the force 
field?? /Any suggestions?

/ That's all.


Your literature searching for similar published work should probably 
have suggested some good options.


Mark
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Re: [gmx-users] MD simulation of Glycoproteion

[Yun Shi]

2011/12/14 陈应广 <525342...@qq.com>

>
> **
>
>
>  Dear gromacs users
>
>  I used Gromacs in order to get a MD simulation of Glycoproteion.now I
> have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a
> Warnning:Fatal error: Residue ""not found in residue topology database.
> And I know it was because of the force field,I want to know which force
> field should be choose in GMX,And where I can get the force field?? *Any
> suggestions?
> *
>

I guess you have to check the residue names, especially those glyco parts,
which are probably not in the force field you chose.


> ** That's all.
>
>
> Thank  you
> **
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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