[gmx-users] problems occur during simulation

[Justin A. Lemkul]

On 6/12/12 3:30 PM, abhidon89 wrote:
> an error occurred while running Grompp
> Atomtype opls_977 not found
> i have named atom type in the pdb file opls_977 for phosphorus .
>

The atom type should not appear in the .pdb file.  If you have added some new 
atom type to the OPLS force field, you need to add its parameters to 
ffnonbonded.itp in order to actually make use of it.

> Second
> how can i make a rtp file ad how is it useful if forcefield residues are not
> found.
>

Following this procedure:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

allows you to solve this error:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

in order to use pdb2gmx to generate the topology.

If you need further help, it would be best to state what you're trying to 
accomplish and what exactly you have done thus far to try to address the problem 
at hand.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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