[gmx-users] want to remove H5T entry form HDB file / open terminal (P, O) for polymerization of i-motif

[Mark Abraham]

On 8/07/2011 11:06 PM, raghav singh wrote:
> Hi Justin, All,
>
> This is my recent log of PDB2GMX command... I have got what I wanted 
> but I would really appreciate if one you experts have a look and let 
> me know weather everything is fine.
>
> I have not calculated new charge distribution after removing the 
> entries for H5T and H3T .. so here I have found non integral charges 
> on molecule.. (which I am going to do right now).

Non-integral total charges are clearly garbage. This issue is just a tip 
of the iceberg of why parameterizing new species is something of an 
expert topic.

Mark