[gmx-users] PDB file that can be read in Gromacs

[paul buscemi]

As Justin has pointed out , this process is well documented and UNL is not often found in molecules. No matter what - you will have to do some leg work.   Because I run into this almost daily, this may at least get you started. First try using x2top with a selected force field.  If your molecule is not too strange, there is a good chance  the force field will recognize it.  If not, then modify or  generate the n2t file  ( found in the ff folder ) and again, if the molecule is ‘normal’ only a few atom types may need to be made. Then convert the top file to itp if you wish.   If you can use gromos54a7 ff  then try  using ATB to generate an itp ( which may not be a full QM file )  

good luck
Paul 

> On Mar 14, 2019, at 2:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 3/14/19 3:21 PM, Phuong Chau wrote:
>> Hello everyone,
>> 
>> I want to generate gromacs topology of a substance (a single chemical)
>> which has a pdb file generated by RDKIT from SMILES representation of that
>> substance (MolToPDBFile). However, when I input the pdb file generated by
>> RDKit, it showed the error of "Residue 'UNL' not found in residue topology
>> database".
>> 
>> The general idea is:
>> Input: Name of a substance (single chemical)
>> Output: pdb file of the substance (does not have to be generated by RDKit)
>> and the topology file of its susbtance that is generated by Gromacs.
>> 
>> Could anyone tell me any possible solution to solve this problem?
> 
> pdb2gmx isn't magic :)
> 
> http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database
> 
> -Justin
> 
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