[gmx-users] Question Regarding GMX Grompp Unknown Atom Type

Elise White elisenwhite at gmail.com
Thu Feb 9 16:54:34 CET 2017

Hello again,

I was amidst inserting a protein into a POPG lipid bilayer using the
Gromos96 53a6
force field when I ran into a rather tricky problem -

An error message popped up that said, "Unknown atom type: HO."

I have performed all the modifications necessary to expand my force field
to accommodate
the lipid bilayer, and this atom type does not seem to appear anywhere
under my bilayer's 'atom types' heading, 'non bond param' heading or 'pair
type' heading in the ffnonbonded.itp file.

I did notice, however, that this atom type does appear twice in my lipid
bilayer's topology file and
I am wondering if you have any suggestions as to how to either remove it or
accommodate it.

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
     1     HO        1    POPG      H1       0         0.3980   1.0080 ;
     2     OA        1    POPG      O2       0        -0.5480   15.9994 ;
     3     HO        1    POPG      H3       1         0.3980   1.0080 ;
     4     CH2       1    POPG      C4       0         0.1500   14.0270 ;


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