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
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