[gmx-users] Coordinate file does not match topology

[Yang Ye]

On 6/11/2007 4:27 AM, David van der Spoel wrote:
> Sheyore Omovie wrote:
>> Thanks Yang,
>> Each of the residues in my *.gro have more H-atoms than in *.top. I 
>> added the 21 H-atoms in [molecules] section of *.top. But grompp 
>> still came up with the ff error: No such molecule type.
>> Do i have to edit [moleculetype] section too?
>> Rgds
>> John
>>
>>
>
> Please do not edit the topology file unless you are very sure what you 
> are doing. You probably select a united atom force field and want to 
> combine it with an all atom coordinate file. You will have to use the 
> conf.gro that pdb2gmx produces.
Hi, Omovie

Hope David's comment help you to understand what you are doing with the 
step of grompp. No individual H-atom shall exist outside a molecule as 
we are not doing nuclear simulation. =)

Regards,
Yang Ye